HEADER HYDROLASE 08-NOV-18 6N1A TITLE CRYSTAL STRUCTURE OF AN N-ACETYLGALACTOSAMINE DEACETYLASE FROM F. TITLE 2 PLAUTII 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS N-ACETYLGALACTOSAMINE DEACETYLASE, A BLOOD ANTIGEN, CAZY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.SIM,P.RAHFELD,S.G.WITHERS REVDAT 4 08-JAN-20 6N1A 1 REMARK REVDAT 3 04-SEP-19 6N1A 1 JRNL REVDAT 2 10-JUL-19 6N1A 1 JRNL REVDAT 1 12-JUN-19 6N1A 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 46465 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2406 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2765 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 139 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3070 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 363 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.30000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -0.40000 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): 0.074 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.075 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 : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3207 ; 0.021 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2696 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4389 ; 1.942 ; 1.930 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6282 ; 3.812 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 395 ; 7.242 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 171 ;35.762 ;24.620 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 459 ;12.675 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;11.350 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 449 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3680 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 686 ; 0.019 ; 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): 1553 ; 1.507 ; 1.717 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1552 ; 1.506 ; 1.716 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1942 ; 2.086 ; 2.572 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 6N1A 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_1000237943. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-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) : 0.9194 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 : 48937 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 46.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 22.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.2 REMARK 200 DATA REDUNDANCY IN SHELL : 13.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: CRANK2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CACL2, 0.1 M MES PH 6.0, 18% PEG REMARK 280 4000, AND 20 MM MNCL2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 25.79200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.16250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.59300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.16250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.79200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.59300 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 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 -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS 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 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 ALA A 1 REMARK 465 ASP A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 GLU A 5 REMARK 465 ALA A 392 REMARK 465 LEU A 393 REMARK 465 VAL A 394 REMARK 465 SER A 395 REMARK 465 GLY A 396 REMARK 465 ASN A 397 REMARK 465 SER A 398 REMARK 465 LEU A 399 REMARK 465 MET A 400 REMARK 465 LEU A 401 REMARK 465 SER A 402 REMARK 465 ALA A 403 REMARK 465 GLU A 404 REMARK 465 THR A 405 REMARK 465 THR A 406 REMARK 465 SER A 407 REMARK 465 LEU A 408 REMARK 465 PRO A 409 REMARK 465 THR A 410 REMARK 465 GLY A 411 REMARK 465 ASP A 412 REMARK 465 VAL A 413 REMARK 465 MET A 414 REMARK 465 LYS A 415 REMARK 465 LEU A 416 REMARK 465 GLU A 417 REMARK 465 THR A 418 REMARK 465 SER A 419 REMARK 465 PHE A 420 REMARK 465 ALA A 421 REMARK 465 PRO A 422 REMARK 465 VAL A 423 REMARK 465 ASP A 424 REMARK 465 THR A 425 REMARK 465 SER A 426 REMARK 465 ASP A 427 REMARK 465 GLN A 428 REMARK 465 VAL A 429 REMARK 465 VAL A 430 REMARK 465 LYS A 431 REMARK 465 TYR A 432 REMARK 465 THR A 433 REMARK 465 SER A 434 REMARK 465 SER A 435 REMARK 465 ASP A 436 REMARK 465 PRO A 437 REMARK 465 ASP A 438 REMARK 465 VAL A 439 REMARK 465 ALA A 440 REMARK 465 THR A 441 REMARK 465 VAL A 442 REMARK 465 ASP A 443 REMARK 465 GLU A 444 REMARK 465 PHE A 445 REMARK 465 GLY A 446 REMARK 465 THR A 447 REMARK 465 ILE A 448 REMARK 465 THR A 449 REMARK 465 GLY A 450 REMARK 465 VAL A 451 REMARK 465 SER A 452 REMARK 465 VAL A 453 REMARK 465 GLY A 454 REMARK 465 SER A 455 REMARK 465 ALA A 456 REMARK 465 ARG A 457 REMARK 465 ILE A 458 REMARK 465 MET A 459 REMARK 465 ALA A 460 REMARK 465 GLU A 461 REMARK 465 THR A 462 REMARK 465 ARG A 463 REMARK 465 GLU A 464 REMARK 465 GLY A 465 REMARK 465 LEU A 466 REMARK 465 SER A 467 REMARK 465 ASP A 468 REMARK 465 ASP A 469 REMARK 465 LEU A 470 REMARK 465 GLU A 471 REMARK 465 ILE A 472 REMARK 465 ALA A 473 REMARK 465 VAL A 474 REMARK 465 VAL A 475 REMARK 465 GLU A 476 REMARK 465 ASN A 477 REMARK 465 PRO A 478 REMARK 465 TYR A 479 REMARK 465 THR A 480 REMARK 465 LEU A 481 REMARK 465 ILE A 482 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 OE1 GLU A 230 O HOH A 601 1.98 REMARK 500 O HOH A 633 O HOH A 952 2.14 REMARK 500 OE2 GLU A 168 O HOH A 602 2.15 REMARK 500 O HOH A 623 O HOH A 954 2.16 REMARK 500 O HOH A 837 O HOH A 842 2.17 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 SER A 374 CB SER A 374 OG -0.080 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 ARG A 132 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 MET A 183 CG - SD - CE ANGL. DEV. = 11.4 DEGREES REMARK 500 ASP A 192 CB - CG - OD1 ANGL. DEV. = 10.4 DEGREES REMARK 500 ASP A 192 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG A 194 NH1 - CZ - NH2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 194 NE - CZ - NH1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 194 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 195 CB - CG - OD2 ANGL. DEV. = 5.5 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 58 -26.53 83.86 REMARK 500 ASP A 72 -0.58 -142.50 REMARK 500 VAL A 74 -53.18 -128.78 REMARK 500 MET A 183 52.02 -142.77 REMARK 500 ASP A 195 65.33 64.31 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 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 35 OD1 REMARK 620 2 ASP A 35 OD2 52.1 REMARK 620 3 ASP A 101 OD1 78.9 74.7 REMARK 620 4 ASP A 253 OD1 80.5 130.1 82.7 REMARK 620 5 HOH A 637 O 157.2 143.8 90.2 78.3 REMARK 620 6 HOH A 653 O 87.9 111.9 156.7 76.3 95.0 REMARK 620 7 HOH A 645 O 127.9 76.2 82.4 144.0 69.2 120.7 REMARK 620 8 HOH A 819 O 91.2 64.8 134.6 139.6 110.4 63.9 69.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CSD A 98 OD1 REMARK 620 2 ASP A 99 OD1 86.5 REMARK 620 3 HIS A 251 NE2 176.4 90.5 REMARK 620 4 HOH A 666 O 88.4 174.9 94.5 REMARK 620 5 HOH A 712 O 91.9 88.2 90.0 92.2 REMARK 620 6 HOH A 786 O 83.9 85.0 93.8 94.2 172.2 REMARK 620 N 1 2 3 4 5 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 192 O REMARK 620 2 ASP A 192 OD1 73.4 REMARK 620 3 ASP A 195 OD1 82.5 80.1 REMARK 620 4 ASP A 195 OD2 93.7 130.5 50.6 REMARK 620 5 HOH A 859 O 149.5 78.7 80.8 95.2 REMARK 620 6 HOH A 846 O 84.0 79.2 157.8 148.2 102.8 REMARK 620 7 HOH A 693 O 60.6 131.3 107.2 70.5 149.4 81.1 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 506 DBREF1 6N1A A 1 482 UNP A0A1C7FP65_9FIRM DBREF2 6N1A A A0A1C7FP65 28 509 SEQADV 6N1A MET A -20 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A GLY A -19 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A SER A -18 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A SER A -17 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A HIS A -16 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A HIS A -15 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A HIS A -14 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A HIS A -13 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A HIS A -12 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A HIS A -11 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A SER A -10 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A SER A -9 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A GLY A -8 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A LEU A -7 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A VAL A -6 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A PRO A -5 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A ARG A -4 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A GLY A -3 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A SER A -2 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A HIS A -1 UNP A0A1C7FP6 EXPRESSION TAG SEQADV 6N1A MET A 0 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 CSD 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 MODRES 6N1A CSD A 98 CYS MODIFIED RESIDUE HET CSD A 98 8 HET MN A 501 1 HET CA A 502 1 HET CA A 503 1 HET GOL A 504 6 HET GOL A 505 6 HET GOL A 506 6 HETNAM CSD 3-SULFINOALANINE HETNAM MN MANGANESE (II) ION HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CSD C3 H7 N O4 S FORMUL 2 MN MN 2+ FORMUL 3 CA 2(CA 2+) FORMUL 5 GOL 3(C3 H8 O3) FORMUL 8 HOH *363(H2 O) HELIX 1 AA1 SER A 158 ARG A 162 5 5 HELIX 2 AA2 GLY A 208 ASN A 215 5 8 HELIX 3 AA3 PRO A 258 LYS A 261 5 4 HELIX 4 AA4 PHE A 375 ASP A 384 1 10 SHEET 1 AA1 4 ASN A 9 LYS A 10 0 SHEET 2 AA1 4 ARG A 364 SER A 374 -1 O GLU A 372 N ASN A 9 SHEET 3 AA1 4 THR A 330 LYS A 340 -1 N TYR A 335 O GLY A 369 SHEET 4 AA1 4 GLN A 312 GLU A 321 -1 N GLU A 321 O THR A 330 SHEET 1 AA2 3 VAL A 31 TRP A 43 0 SHEET 2 AA2 3 TYR A 46 PRO A 54 -1 O TRP A 49 N VAL A 37 SHEET 3 AA2 3 SER A 66 SER A 70 -1 O VAL A 68 N ALA A 50 SHEET 1 AA3 4 TYR A 95 ASN A 105 0 SHEET 2 AA3 4 ALA A 110 ASP A 119 -1 O ALA A 110 N ASN A 105 SHEET 3 AA3 4 ALA A 127 SER A 134 -1 O ARG A 132 N ALA A 113 SHEET 4 AA3 4 ILE A 172 SER A 177 -1 O ILE A 175 N VAL A 129 SHEET 1 AA4 2 VAL A 142 PRO A 143 0 SHEET 2 AA4 2 VAL A 164 ALA A 165 -1 O ALA A 165 N VAL A 142 SHEET 1 AA5 2 TYR A 146 ASP A 147 0 SHEET 2 AA5 2 VAL A 152 TRP A 153 -1 O VAL A 152 N ASP A 147 SHEET 1 AA6 4 LEU A 184 ASP A 191 0 SHEET 2 AA6 4 VAL A 196 ASN A 203 -1 O VAL A 196 N ASP A 191 SHEET 3 AA6 4 PHE A 216 SER A 222 -1 O SER A 222 N PHE A 197 SHEET 4 AA6 4 VAL A 232 ARG A 233 -1 O VAL A 232 N MET A 219 SHEET 1 AA7 4 ALA A 248 VAL A 257 0 SHEET 2 AA7 4 GLU A 262 PHE A 270 -1 O PHE A 270 N ALA A 248 SHEET 3 AA7 4 VAL A 279 SER A 285 -1 O SER A 285 N PHE A 263 SHEET 4 AA7 4 TRP A 291 GLN A 293 -1 O GLU A 292 N THR A 284 SHEET 1 AA8 2 MET A 346 VAL A 347 0 SHEET 2 AA8 2 ILE A 356 GLN A 357 -1 O ILE A 356 N VAL A 347 LINK OD1 ASP A 35 CA CA A 503 1555 1555 2.44 LINK OD2 ASP A 35 CA CA A 503 1555 1555 2.59 LINK C ASN A 97 N CSD A 98 1555 1555 1.33 LINK C CSD A 98 N ASP A 99 1555 1555 1.31 LINK OD1 CSD A 98 MN MN A 501 1555 1555 2.12 LINK OD1 ASP A 99 MN MN A 501 1555 1555 2.11 LINK OD1 ASP A 101 CA CA A 503 1555 1555 2.49 LINK O ASP A 192 CA CA A 502 1555 1555 2.62 LINK OD1 ASP A 192 CA CA A 502 1555 1555 2.39 LINK OD1 ASP A 195 CA CA A 502 1555 1555 2.49 LINK OD2 ASP A 195 CA CA A 502 1555 1555 2.70 LINK NE2 HIS A 251 MN MN A 501 1555 1555 2.15 LINK OD1 ASP A 253 CA CA A 503 1555 1555 2.34 LINK MN MN A 501 O HOH A 666 1555 1555 2.10 LINK MN MN A 501 O HOH A 712 1555 1555 2.19 LINK MN MN A 501 O HOH A 786 1555 1555 2.11 LINK CA CA A 502 O HOH A 859 1555 1555 2.40 LINK CA CA A 503 O HOH A 637 1555 1555 2.42 LINK CA CA A 503 O HOH A 653 1555 1555 2.29 LINK CA CA A 503 O HOH A 645 1555 1555 2.38 LINK CA CA A 503 O HOH A 819 1555 1555 2.82 LINK CA CA A 502 O HOH A 846 1555 4555 2.43 LINK CA CA A 502 O HOH A 693 1555 4555 2.75 CISPEP 1 ASN A 84 PRO A 85 0 -1.17 SITE 1 AC1 6 CSD A 98 ASP A 99 HIS A 251 HOH A 666 SITE 2 AC1 6 HOH A 712 HOH A 786 SITE 1 AC2 6 ASP A 192 ASP A 195 ASN A 235 HOH A 693 SITE 2 AC2 6 HOH A 846 HOH A 859 SITE 1 AC3 7 ASP A 35 ASP A 101 ASP A 253 HOH A 637 SITE 2 AC3 7 HOH A 645 HOH A 653 HOH A 819 SITE 1 AC4 8 ASN A 55 SER A 60 GLU A 63 HIS A 96 SITE 2 AC4 8 CSD A 98 HOH A 666 HOH A 671 HOH A 870 SITE 1 AC5 6 ALA A 11 PRO A 12 GLY A 13 SER A 307 SITE 2 AC5 6 TRP A 308 ASP A 309 SITE 1 AC6 6 TYR A 104 ASN A 105 ALA A 106 GLU A 107 SITE 2 AC6 6 TYR A 190 HOH A 680 CRYST1 51.584 69.186 104.325 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 0.019386 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014454 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009585 0.00000