HEADER HYDROLASE 08-NOV-18 6N1B TITLE CRYSTAL STRUCTURE OF AN N-ACETYLGALACTOSAMINE DEACETYLASE FROM F. TITLE 2 PLAUTII IN COMPLEX WITH BLOOD GROUP B TRISACCHARIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBOHYDRATE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: N-ACETYLGALACTOSAMINE DEACETYLASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FLAVONIFRACTOR PLAUTII; SOURCE 3 ORGANISM_TAXID: 292800; SOURCE 4 GENE: A4U99_12080; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS N-ACETYLGALACTOSAMINE DEACETYLASE, A BLOOD ANTIGEN, CAZY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.SIM,P.RAHFELD,S.G.WITHERS REVDAT 6 11-OCT-23 6N1B 1 HETSYN LINK REVDAT 5 29-JUL-20 6N1B 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 08-JAN-20 6N1B 1 REMARK REVDAT 3 04-SEP-19 6N1B 1 JRNL REVDAT 2 10-JUL-19 6N1B 1 JRNL REVDAT 1 12-JUN-19 6N1B 0 JRNL AUTH P.RAHFELD,L.SIM,H.MOON,I.CONSTANTINESCU,C.MORGAN-LANG, JRNL AUTH 2 S.J.HALLAM,J.N.KIZHAKKEDATHU,S.G.WITHERS JRNL TITL AN ENZYMATIC PATHWAY IN THE HUMAN GUT MICROBIOME THAT JRNL TITL 2 CONVERTS A TO UNIVERSAL O TYPE BLOOD. JRNL REF NAT MICROBIOL V. 4 1475 2019 JRNL REFN ESSN 2058-5276 JRNL PMID 31182795 JRNL DOI 10.1038/S41564-019-0469-7 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 86066 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4530 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4631 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 244 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3061 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 359 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.31000 REMARK 3 B22 (A**2) : -0.40000 REMARK 3 B33 (A**2) : 0.71000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.043 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.044 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3217 ; 0.027 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2696 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4403 ; 2.227 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6289 ; 3.887 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 390 ; 7.616 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;34.885 ;24.675 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 456 ;12.515 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;14.482 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 460 ; 0.167 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3649 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 680 ; 0.026 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1545 ; 1.331 ; 1.089 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1544 ; 1.317 ; 1.088 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1931 ; 1.814 ; 1.644 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6N1B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000237971. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 90596 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 46.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 6N1A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CACL2, 0.1 M MES PH 6.0, 18% PEG REMARK 280 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 25.85500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.40500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.62000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.40500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.85500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.62000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 GLU A 6 REMARK 465 PRO A 392 REMARK 465 ALA A 393 REMARK 465 LEU A 394 REMARK 465 VAL A 395 REMARK 465 SER A 396 REMARK 465 GLY A 397 REMARK 465 ASN A 398 REMARK 465 SER A 399 REMARK 465 LEU A 400 REMARK 465 MET A 401 REMARK 465 LEU A 402 REMARK 465 SER A 403 REMARK 465 ALA A 404 REMARK 465 GLU A 405 REMARK 465 THR A 406 REMARK 465 THR A 407 REMARK 465 SER A 408 REMARK 465 LEU A 409 REMARK 465 PRO A 410 REMARK 465 THR A 411 REMARK 465 GLY A 412 REMARK 465 ASP A 413 REMARK 465 VAL A 414 REMARK 465 MET A 415 REMARK 465 LYS A 416 REMARK 465 LEU A 417 REMARK 465 GLU A 418 REMARK 465 THR A 419 REMARK 465 SER A 420 REMARK 465 PHE A 421 REMARK 465 ALA A 422 REMARK 465 PRO A 423 REMARK 465 VAL A 424 REMARK 465 ASP A 425 REMARK 465 THR A 426 REMARK 465 SER A 427 REMARK 465 ASP A 428 REMARK 465 GLN A 429 REMARK 465 VAL A 430 REMARK 465 VAL A 431 REMARK 465 LYS A 432 REMARK 465 TYR A 433 REMARK 465 THR A 434 REMARK 465 SER A 435 REMARK 465 SER A 436 REMARK 465 ASP A 437 REMARK 465 PRO A 438 REMARK 465 ASP A 439 REMARK 465 VAL A 440 REMARK 465 ALA A 441 REMARK 465 THR A 442 REMARK 465 VAL A 443 REMARK 465 ASP A 444 REMARK 465 GLU A 445 REMARK 465 PHE A 446 REMARK 465 GLY A 447 REMARK 465 THR A 448 REMARK 465 ILE A 449 REMARK 465 THR A 450 REMARK 465 GLY A 451 REMARK 465 VAL A 452 REMARK 465 SER A 453 REMARK 465 VAL A 454 REMARK 465 GLY A 455 REMARK 465 SER A 456 REMARK 465 ALA A 457 REMARK 465 ARG A 458 REMARK 465 ILE A 459 REMARK 465 MET A 460 REMARK 465 ALA A 461 REMARK 465 GLU A 462 REMARK 465 THR A 463 REMARK 465 ARG A 464 REMARK 465 GLU A 465 REMARK 465 GLY A 466 REMARK 465 LEU A 467 REMARK 465 SER A 468 REMARK 465 ASP A 469 REMARK 465 ASP A 470 REMARK 465 LEU A 471 REMARK 465 GLU A 472 REMARK 465 ILE A 473 REMARK 465 ALA A 474 REMARK 465 VAL A 475 REMARK 465 VAL A 476 REMARK 465 GLU A 477 REMARK 465 ASN A 478 REMARK 465 PRO A 479 REMARK 465 TYR A 480 REMARK 465 THR A 481 REMARK 465 LEU A 482 REMARK 465 ILE A 483 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 99 O HOH A 615 1.71 REMARK 500 SG CYS A 99 O3 GLA B 3 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 739 O HOH A 879 4455 2.18 REMARK 500 O HOH A 873 O HOH A 938 4545 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 41 CD GLU A 41 OE1 0.071 REMARK 500 GLU A 149 CG GLU A 149 CD 0.092 REMARK 500 GLU A 149 CD GLU A 149 OE1 0.172 REMARK 500 GLU A 149 CD GLU A 149 OE2 0.073 REMARK 500 MET A 150 CG MET A 150 SD -0.176 REMARK 500 MET A 184 CB MET A 184 CG -0.194 REMARK 500 ARG A 195 CZ ARG A 195 NH1 0.100 REMARK 500 VAL A 233 CA VAL A 233 CB -0.164 REMARK 500 ARG A 234 CZ ARG A 234 NH1 -0.086 REMARK 500 GLU A 293 CD GLU A 293 OE1 -0.116 REMARK 500 SER A 375 CB SER A 375 OG -0.095 REMARK 500 ASP A 385 CB ASP A 385 CG -0.137 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE A 18 CB - CG - CD1 ANGL. DEV. = 5.1 DEGREES REMARK 500 TYR A 63 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 TYR A 136 CB - CG - CD2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP A 160 CB - CG - OD2 ANGL. DEV. = -10.5 DEGREES REMARK 500 ASP A 193 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 195 NH1 - CZ - NH2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 195 NE - CZ - NH2 ANGL. DEV. = -10.5 DEGREES REMARK 500 ARG A 234 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 306 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 311 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP A 311 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 TYR A 315 CB - CG - CD2 ANGL. DEV. = 5.2 DEGREES REMARK 500 TYR A 315 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP A 350 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 365 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 365 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP A 385 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 59 -25.66 85.96 REMARK 500 VAL A 75 -53.57 -129.21 REMARK 500 MET A 184 43.43 -141.24 REMARK 500 ASP A 196 68.16 66.85 REMARK 500 ASN A 345 19.29 56.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 131 0.08 SIDE CHAIN REMARK 500 ARG A 195 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 36 OD1 REMARK 620 2 ASP A 36 OD2 52.4 REMARK 620 3 ASP A 102 OD1 78.5 74.5 REMARK 620 4 ASP A 254 OD1 79.7 129.3 81.4 REMARK 620 5 HOH A 617 O 87.8 113.9 154.2 74.6 REMARK 620 6 HOH A 674 O 129.2 77.3 82.8 142.9 122.4 REMARK 620 7 HOH A 676 O 156.5 143.4 89.7 78.5 94.7 68.0 REMARK 620 8 HOH A 805 O 92.0 65.2 134.7 140.8 66.8 69.3 110.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 100 OD1 REMARK 620 2 HOH A 602 O 166.2 REMARK 620 3 HOH A 615 O 98.8 67.8 REMARK 620 4 HOH A 696 O 91.4 92.1 90.8 REMARK 620 5 HOH A 702 O 82.6 93.4 88.6 173.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 193 O REMARK 620 2 ASP A 193 OD1 72.9 REMARK 620 3 ASP A 196 OD1 84.4 76.6 REMARK 620 4 ASP A 196 OD2 100.8 127.7 51.1 REMARK 620 5 HOH A 655 O 36.5 82.5 51.4 67.9 REMARK 620 6 HOH A 843 O 40.1 89.3 52.0 62.3 6.8 REMARK 620 7 HOH A 866 O 33.7 90.0 59.6 67.5 10.0 7.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 504 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 196 O REMARK 620 2 ASP A 224 OD1 124.3 REMARK 620 3 HOH A 616 O 47.5 91.6 REMARK 620 4 HOH A 649 O 51.4 86.1 5.5 REMARK 620 5 HOH A 717 O 52.0 85.8 5.8 0.6 REMARK 620 6 HOH A 761 O 54.2 88.9 7.4 7.8 7.5 REMARK 620 7 HOH A 921 O 52.4 89.5 5.4 6.3 6.1 2.1 REMARK 620 N 1 2 3 4 5 6 DBREF1 6N1B A 2 483 UNP A0A1C7FP65_9FIRM DBREF2 6N1B A A0A1C7FP65 28 509 SEQADV 6N1B MET A -19 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B GLY A -18 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B SER A -17 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B SER A -16 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B HIS A -15 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B HIS A -14 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B HIS A -13 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B HIS A -12 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B HIS A -11 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B HIS A -10 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B SER A -9 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B SER A -8 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B GLY A -7 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B LEU A -6 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B VAL A -5 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B PRO A -4 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B ARG A -3 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B GLY A -2 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B SER A -1 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B HIS A 0 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1B MET A 1 UNP A0A1C7FP6 EXPRESSION TAG SEQRES 1 A 503 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 503 LEU VAL PRO ARG GLY SER HIS MET ALA ASP SER SER GLU SEQRES 3 A 503 SER ALA LEU ASN LYS ALA PRO GLY TYR GLN ASP PHE PRO SEQRES 4 A 503 ALA TYR TYR SER ASP SER ALA HIS ALA ASP ASP GLN VAL SEQRES 5 A 503 THR HIS PRO ASP VAL VAL VAL LEU GLU GLU PRO TRP ASN SEQRES 6 A 503 GLY TYR ARG TYR TRP ALA VAL TYR THR PRO ASN VAL MET SEQRES 7 A 503 ARG ILE SER ILE TYR GLU ASN PRO SER ILE VAL ALA SER SEQRES 8 A 503 SER ASP GLY VAL HIS TRP VAL GLU PRO GLU GLY LEU SER SEQRES 9 A 503 ASN PRO ILE GLU PRO GLN PRO PRO SER THR ARG TYR HIS SEQRES 10 A 503 ASN CYS ASP ALA ASP MET VAL TYR ASN ALA GLU TYR ASP SEQRES 11 A 503 ALA MET MET ALA TYR TRP ASN TRP ALA ASP ASP GLN GLY SEQRES 12 A 503 GLY GLY VAL GLY ALA GLU VAL ARG LEU ARG ILE SER TYR SEQRES 13 A 503 ASP GLY VAL HIS TRP GLY VAL PRO VAL THR TYR ASP GLU SEQRES 14 A 503 MET THR ARG VAL TRP SER LYS PRO THR SER ASP ALA GLU SEQRES 15 A 503 ARG GLN VAL ALA ASP GLY GLU ASP ASP PHE ILE THR ALA SEQRES 16 A 503 ILE ALA SER PRO ASP ARG TYR ASP MET LEU SER PRO THR SEQRES 17 A 503 ILE VAL TYR ASP ASP PHE ARG ASP VAL PHE ILE LEU TRP SEQRES 18 A 503 ALA ASN ASN THR GLY ASP VAL GLY TYR GLN ASN GLY GLN SEQRES 19 A 503 ALA ASN PHE VAL GLU MET ARG TYR SER ASP ASP GLY ILE SEQRES 20 A 503 THR TRP GLY GLU PRO VAL ARG VAL ASN GLY PHE LEU GLY SEQRES 21 A 503 LEU ASP GLU ASN GLY GLN GLN LEU ALA PRO TRP HIS GLN SEQRES 22 A 503 ASP VAL GLN TYR VAL PRO ASP LEU LYS GLU PHE VAL CYS SEQRES 23 A 503 ILE SER GLN CYS PHE ALA GLY ARG ASN PRO ASP GLY SER SEQRES 24 A 503 VAL LEU HIS LEU THR THR SER LYS ASP GLY VAL ASN TRP SEQRES 25 A 503 GLU GLN VAL GLY THR LYS PRO LEU LEU SER PRO GLY PRO SEQRES 26 A 503 ASP GLY SER TRP ASP ASP PHE GLN ILE TYR ARG SER SER SEQRES 27 A 503 PHE TYR TYR GLU PRO GLY SER SER ALA GLY ASP GLY THR SEQRES 28 A 503 MET ARG VAL TRP TYR SER ALA LEU GLN LYS ASP THR ASN SEQRES 29 A 503 ASN LYS MET VAL ALA ASP SER SER GLY ASN LEU THR ILE SEQRES 30 A 503 GLN ALA LYS SER GLU ASP ASP ARG ILE TRP ARG ILE GLY SEQRES 31 A 503 TYR ALA GLU ASN SER PHE VAL GLU MET MET ARG VAL LEU SEQRES 32 A 503 LEU ASP ASP PRO GLY TYR THR THR PRO ALA LEU VAL SER SEQRES 33 A 503 GLY ASN SER LEU MET LEU SER ALA GLU THR THR SER LEU SEQRES 34 A 503 PRO THR GLY ASP VAL MET LYS LEU GLU THR SER PHE ALA SEQRES 35 A 503 PRO VAL ASP THR SER ASP GLN VAL VAL LYS TYR THR SER SEQRES 36 A 503 SER ASP PRO ASP VAL ALA THR VAL ASP GLU PHE GLY THR SEQRES 37 A 503 ILE THR GLY VAL SER VAL GLY SER ALA ARG ILE MET ALA SEQRES 38 A 503 GLU THR ARG GLU GLY LEU SER ASP ASP LEU GLU ILE ALA SEQRES 39 A 503 VAL VAL GLU ASN PRO TYR THR LEU ILE HET GAL B 1 12 HET FUC B 2 10 HET GLA B 3 11 HET CA A 501 1 HET CA A 502 1 HET CA A 503 1 HET CA A 504 1 HET GOL A 508 6 HET GOL A 509 6 HET GOL A 510 6 HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GAL C6 H12 O6 FORMUL 2 FUC C6 H12 O5 FORMUL 2 GLA C6 H12 O6 FORMUL 3 CA 4(CA 2+) FORMUL 7 GOL 3(C3 H8 O3) FORMUL 10 HOH *359(H2 O) HELIX 1 AA1 SER A 159 ARG A 163 5 5 HELIX 2 AA2 GLY A 209 ASN A 216 5 8 HELIX 3 AA3 PRO A 259 LYS A 262 5 4 HELIX 4 AA4 PHE A 376 ASP A 385 1 10 SHEET 1 AA1 4 ASN A 10 LYS A 11 0 SHEET 2 AA1 4 ARG A 365 SER A 375 -1 O GLU A 373 N ASN A 10 SHEET 3 AA1 4 THR A 331 LYS A 341 -1 N TYR A 336 O GLY A 370 SHEET 4 AA1 4 GLN A 313 GLU A 322 -1 N GLU A 322 O THR A 331 SHEET 1 AA2 3 VAL A 32 TRP A 44 0 SHEET 2 AA2 3 TYR A 47 PRO A 55 -1 O TRP A 50 N VAL A 38 SHEET 3 AA2 3 SER A 67 SER A 71 -1 O VAL A 69 N ALA A 51 SHEET 1 AA3 4 TYR A 96 ASN A 106 0 SHEET 2 AA3 4 ALA A 111 ASP A 120 -1 O ALA A 111 N ASN A 106 SHEET 3 AA3 4 ALA A 128 SER A 135 -1 O ARG A 133 N ALA A 114 SHEET 4 AA3 4 ILE A 173 SER A 178 -1 O ILE A 173 N LEU A 132 SHEET 1 AA4 2 VAL A 143 PRO A 144 0 SHEET 2 AA4 2 VAL A 165 ALA A 166 -1 O ALA A 166 N VAL A 143 SHEET 1 AA5 2 TYR A 147 ASP A 148 0 SHEET 2 AA5 2 VAL A 153 TRP A 154 -1 O VAL A 153 N ASP A 148 SHEET 1 AA6 4 LEU A 185 ASP A 192 0 SHEET 2 AA6 4 VAL A 197 ASN A 204 -1 O VAL A 197 N ASP A 192 SHEET 3 AA6 4 PHE A 217 SER A 223 -1 O SER A 223 N PHE A 198 SHEET 4 AA6 4 VAL A 233 ARG A 234 -1 O VAL A 233 N MET A 220 SHEET 1 AA7 4 ALA A 249 VAL A 258 0 SHEET 2 AA7 4 GLU A 263 PHE A 271 -1 O VAL A 265 N GLN A 256 SHEET 3 AA7 4 VAL A 280 SER A 286 -1 O SER A 286 N PHE A 264 SHEET 4 AA7 4 GLU A 293 GLN A 294 -1 O GLU A 293 N THR A 285 SHEET 1 AA8 2 MET A 347 ALA A 349 0 SHEET 2 AA8 2 LEU A 355 GLN A 358 -1 O ILE A 357 N VAL A 348 LINK O2 GAL B 1 C1 FUC B 2 1555 1555 1.46 LINK O3 GAL B 1 C1 GLA B 3 1555 1555 1.43 LINK OD1 ASP A 36 CA CA A 502 1555 1555 2.44 LINK OD2 ASP A 36 CA CA A 502 1555 1555 2.57 LINK OD1 ASP A 100 CA CA A 501 1555 1555 1.96 LINK OD1 ASP A 102 CA CA A 502 1555 1555 2.44 LINK O ASP A 193 CA CA A 503 1555 4555 2.43 LINK OD1 ASP A 193 CA CA A 503 1555 4555 2.47 LINK OD1 ASP A 196 CA CA A 503 1555 4555 2.44 LINK OD2 ASP A 196 CA CA A 503 1555 4555 2.59 LINK O ASP A 196 CA CA A 504 1555 4555 2.35 LINK OD1 ASP A 224 CA CA A 504 1555 4555 2.39 LINK OD1 ASP A 254 CA CA A 502 1555 1555 2.42 LINK CA CA A 501 O HOH A 602 1555 1555 2.00 LINK CA CA A 501 O HOH A 615 1555 1555 2.15 LINK CA CA A 501 O HOH A 696 1555 1555 2.14 LINK CA CA A 501 O HOH A 702 1555 1555 2.15 LINK CA CA A 502 O HOH A 617 1555 1555 2.34 LINK CA CA A 502 O HOH A 674 1555 1555 2.44 LINK CA CA A 502 O HOH A 676 1555 1555 2.40 LINK CA CA A 502 O HOH A 805 1555 1555 2.77 LINK CA CA A 503 O HOH A 655 1555 4455 2.48 LINK CA CA A 503 O HOH A 843 1555 1555 2.43 LINK CA CA A 503 O HOH A 866 1555 1555 2.50 LINK CA CA A 504 O HOH A 616 1555 1555 2.43 LINK CA CA A 504 O HOH A 649 1555 4455 2.42 LINK CA CA A 504 O HOH A 717 1555 1555 2.40 LINK CA CA A 504 O HOH A 761 1555 4455 2.41 LINK CA CA A 504 O HOH A 921 1555 4455 2.37 CISPEP 1 ASN A 85 PRO A 86 0 -3.56 CRYST1 51.710 69.240 104.810 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019339 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009541 0.00000