HEADER CELL ADHESION 19-DEC-13 4O5J TITLE CRYSTAL STRUCTURE OF SABA FROM HELICOBACTER PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL EXTRACELLULAR ADHESION DOMAIN, UNP RESIDUES 4- COMPND 5 463; COMPND 6 SYNONYM: SIALIC ACID-BINDING ADHESIN SABA; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85962; SOURCE 4 STRAIN: 26695; SOURCE 5 GENE: C694_03730, SABA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15 KEYWDS TETRATRICOPEPTIDE REPEAT, ADHESIN, CARBOHYDRATE/SUGAR BINDING, OUTER KEYWDS 2 MEMBRANE PROTEIN, HELICOBACTER PYLORI, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR S.S.PANG,S.T.S.NGUYEN,J.C.WHISSTOCK REVDAT 2 26-MAR-14 4O5J 1 JRNL REVDAT 1 01-JAN-14 4O5J 0 JRNL AUTH S.S.PANG,S.T.S.NGUYEN,A.J.PERRY,C.J.DAY,S.PANJIKAR, JRNL AUTH 2 J.TIRALONGO,J.C.WHISSTOCK,T.KWOK JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF THE EXTRACELLULAR JRNL TITL 2 ADHESION DOMAIN OF THE SIALIC ACID-BINDING ADHESIN SABA FROM JRNL TITL 3 HELICOBACTER PYLORI JRNL REF J.BIOL.CHEM. V. 289 6332 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 24375407 JRNL DOI 10.1074/JBC.M113.513135 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 90.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 57908 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) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3062 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4119 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 215 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2839 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : 0.13000 REMARK 3 B12 (A**2) : -0.04000 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): 0.098 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.081 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.433 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2900 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3943 ; 1.533 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 367 ; 4.142 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;40.752 ;26.917 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 476 ;14.509 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;20.571 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 459 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2187 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 2900 ;13.979 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 68 ;63.685 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2943 ;52.249 ; 5.000 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 : MASK 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES: REFINED INDIVIDUALL REMARK 4 REMARK 4 4O5J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-DEC-13. REMARK 100 THE RCSB ID CODE IS RCSB084068. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-13; 13-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON; REMARK 200 AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2; MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537; 0.9690, 0.9795 REMARK 200 MONOCHROMATOR : SI(111); SI(111) REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R; ADSC QUANTUM REMARK 200 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60966 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 90.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.30 REMARK 200 R MERGE FOR SHELL (I) : 1.03000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AUTO-RICKSHAW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 79.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM SODIUM ACETATE, 18-20% PEG 4000, REMARK 280 PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.49000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.98000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 42.98000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.49000 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 GLY A 0 REMARK 465 GLU A 1 REMARK 465 ASP A 2 REMARK 465 ASN A 3 REMARK 465 GLY A 4 REMARK 465 PHE A 5 REMARK 465 PHE A 6 REMARK 465 VAL A 7 REMARK 465 SER A 8 REMARK 465 ALA A 9 REMARK 465 GLY A 10 REMARK 465 TYR A 11 REMARK 465 GLN A 12 REMARK 465 ILE A 13 REMARK 465 GLY A 14 REMARK 465 GLU A 15 REMARK 465 ALA A 16 REMARK 465 VAL A 17 REMARK 465 GLN A 18 REMARK 465 MET A 19 REMARK 465 VAL A 20 REMARK 465 LYS A 21 REMARK 465 ASN A 22 REMARK 465 THR A 23 REMARK 465 GLY A 24 REMARK 465 GLU A 25 REMARK 465 GLY A 114 REMARK 465 ASP A 182 REMARK 465 SER A 183 REMARK 465 THR A 184 REMARK 465 ASN A 400 REMARK 465 GLN A 401 REMARK 465 VAL A 402 REMARK 465 ASN A 403 REMARK 465 THR A 404 REMARK 465 LYS A 405 REMARK 465 ASP A 406 REMARK 465 ILE A 407 REMARK 465 VAL A 408 REMARK 465 THR A 409 REMARK 465 LEU A 410 REMARK 465 PRO A 411 REMARK 465 TYR A 412 REMARK 465 ASP A 413 REMARK 465 LYS A 414 REMARK 465 ASN A 415 REMARK 465 ALA A 416 REMARK 465 PRO A 417 REMARK 465 ALA A 418 REMARK 465 ALA A 419 REMARK 465 GLY A 420 REMARK 465 GLN A 421 REMARK 465 SER A 422 REMARK 465 ASN A 423 REMARK 465 TYR A 424 REMARK 465 GLN A 425 REMARK 465 ILE A 426 REMARK 465 ASN A 427 REMARK 465 PRO A 428 REMARK 465 GLU A 429 REMARK 465 GLN A 430 REMARK 465 GLN A 431 REMARK 465 SER A 432 REMARK 465 ASN A 433 REMARK 465 LEU A 434 REMARK 465 ASN A 435 REMARK 465 GLN A 436 REMARK 465 ALA A 437 REMARK 465 LEU A 438 REMARK 465 ALA A 439 REMARK 465 ALA A 440 REMARK 465 MET A 441 REMARK 465 SER A 442 REMARK 465 ASN A 443 REMARK 465 ASN A 444 REMARK 465 PRO A 445 REMARK 465 PHE A 446 REMARK 465 LYS A 447 REMARK 465 LYS A 448 REMARK 465 VAL A 449 REMARK 465 GLY A 450 REMARK 465 MET A 451 REMARK 465 ILE A 452 REMARK 465 SER A 453 REMARK 465 SER A 454 REMARK 465 GLN A 455 REMARK 465 ASN A 456 REMARK 465 ASN A 457 REMARK 465 ASN A 458 REMARK 465 GLY A 459 REMARK 465 ALA A 460 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 26 CG CD1 CD2 REMARK 470 LYS A 27 CG CD CE NZ REMARK 470 ASN A 28 CG OD1 ND2 REMARK 470 ASP A 115 CG OD1 OD2 REMARK 470 LYS A 168 CG CD CE NZ REMARK 470 SER A 185 OG REMARK 470 SER A 276 OG 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 O3 GOL A 503 O HOH A 699 2.06 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 309 CB SER A 309 OG -0.127 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 359 NE - CZ - NH2 ANGL. DEV. = -3.4 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 LYS A 27 -123.61 72.75 REMARK 500 ALA A 101 -94.38 -125.63 REMARK 500 TYR A 104 103.70 -167.55 REMARK 500 LYS A 112 75.07 -102.41 REMARK 500 VAL A 223 -57.07 -129.86 REMARK 500 THR A 274 105.33 -50.36 REMARK 500 GLN A 277 0.96 -66.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 503 DBREF 4O5J A 1 460 UNP K4NCD9 K4NCD9_HELPY 4 463 SEQADV 4O5J GLY A 0 UNP K4NCD9 EXPRESSION TAG SEQRES 1 A 461 GLY GLU ASP ASN GLY PHE PHE VAL SER ALA GLY TYR GLN SEQRES 2 A 461 ILE GLY GLU ALA VAL GLN MET VAL LYS ASN THR GLY GLU SEQRES 3 A 461 LEU LYS ASN LEU ASN GLU LYS TYR GLU GLN LEU SER GLN SEQRES 4 A 461 TYR LEU ASN GLN VAL ALA SER LEU LYS GLN SER ILE GLN SEQRES 5 A 461 ASN ALA ASN ASN ILE GLU LEU VAL ASN SER SER LEU ASN SEQRES 6 A 461 TYR LEU LYS SER PHE THR ASN ASN ASN TYR ASN SER THR SEQRES 7 A 461 THR GLN SER PRO ILE PHE ASN ALA VAL GLN ALA VAL ILE SEQRES 8 A 461 THR SER VAL LEU GLY PHE TRP SER LEU TYR ALA GLY ASN SEQRES 9 A 461 TYR PHE THR PHE PHE VAL GLY LYS LYS VAL GLY ASP SER SEQRES 10 A 461 GLY GLN PRO ALA SER VAL GLN GLY ASN PRO PRO PHE LYS SEQRES 11 A 461 THR ILE ILE GLU ASN CYS SER GLY ILE GLU ASN CYS ALA SEQRES 12 A 461 MET ASP GLN THR THR TYR ASP LYS MET LYS LYS LEU ALA SEQRES 13 A 461 GLU ASP LEU GLN ALA ALA GLN THR ASN SER ALA THR LYS SEQRES 14 A 461 GLY ASN ASN LEU CYS ALA LEU SER GLY CYS ALA ALA THR SEQRES 15 A 461 ASP SER THR SER ASN PRO PRO ASN SER THR VAL SER ASN SEQRES 16 A 461 ALA LEU ASN LEU ALA GLN GLN LEU MET ASP LEU ILE ALA SEQRES 17 A 461 ASN THR LYS THR ALA MET MET TRP LYS ASN ILE VAL ILE SEQRES 18 A 461 SER GLY VAL SER ASN THR SER GLY ALA ILE THR SER THR SEQRES 19 A 461 ASN TYR PRO THR GLN TYR ALA VAL PHE ASN ASN ILE LYS SEQRES 20 A 461 ALA MET ILE PRO ILE LEU GLN GLN ALA VAL THR LEU SER SEQRES 21 A 461 GLN SER ASN HIS THR LEU SER ALA SER LEU GLN ALA GLN SEQRES 22 A 461 ALA THR GLY SER GLN THR ASN PRO LYS PHE ALA LYS ASP SEQRES 23 A 461 ILE TYR THR PHE ALA GLN ASN GLN LYS GLN VAL ILE SER SEQRES 24 A 461 TYR ALA GLN ASP ILE PHE ASN LEU PHE ASN SER ILE PRO SEQRES 25 A 461 ALA GLU GLN TYR LYS TYR LEU GLU LYS ALA TYR LEU LYS SEQRES 26 A 461 ILE PRO ASN ALA GLY SER THR PRO THR ASN PRO TYR ARG SEQRES 27 A 461 GLN VAL VAL ASN LEU ASN GLN GLU VAL GLN THR ILE LYS SEQRES 28 A 461 ASN ASN VAL SER TYR TYR GLY ASN ARG VAL ASP ALA ALA SEQRES 29 A 461 LEU SER VAL ALA ARG ASP VAL TYR ASN LEU LYS SER ASN SEQRES 30 A 461 GLN ALA GLU ILE VAL THR ALA TYR ASN ASP ALA LYS THR SEQRES 31 A 461 LEU SER GLU GLU ILE SER LYS LEU PRO HIS ASN GLN VAL SEQRES 32 A 461 ASN THR LYS ASP ILE VAL THR LEU PRO TYR ASP LYS ASN SEQRES 33 A 461 ALA PRO ALA ALA GLY GLN SER ASN TYR GLN ILE ASN PRO SEQRES 34 A 461 GLU GLN GLN SER ASN LEU ASN GLN ALA LEU ALA ALA MET SEQRES 35 A 461 SER ASN ASN PRO PHE LYS LYS VAL GLY MET ILE SER SER SEQRES 36 A 461 GLN ASN ASN ASN GLY ALA HET EDO A 501 4 HET EDO A 502 4 HET GOL A 503 6 HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 EDO 2(C2 H6 O2) FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *158(H2 O) HELIX 1 1 LYS A 27 ASN A 54 1 28 HELIX 2 2 ASN A 55 SER A 76 1 22 HELIX 3 3 SER A 80 ALA A 101 1 22 HELIX 4 4 PHE A 128 CYS A 135 1 8 HELIX 5 5 ASP A 144 THR A 163 1 20 HELIX 6 6 THR A 191 THR A 209 1 19 HELIX 7 7 LYS A 216 ILE A 218 5 3 HELIX 8 8 TYR A 235 GLN A 238 5 4 HELIX 9 9 TYR A 239 SER A 268 1 30 HELIX 10 10 GLY A 275 THR A 278 5 4 HELIX 11 11 ASN A 279 SER A 309 1 31 HELIX 12 12 PRO A 311 LYS A 320 1 10 HELIX 13 13 ALA A 321 LYS A 324 5 4 HELIX 14 14 TYR A 336 VAL A 340 5 5 HELIX 15 15 ASN A 341 LYS A 396 1 56 SHEET 1 A 3 GLY A 117 PRO A 119 0 SHEET 2 A 3 PHE A 108 LYS A 112 -1 N LYS A 111 O GLN A 118 SHEET 3 A 3 ALA A 142 MET A 143 1 O MET A 143 N PHE A 108 SHEET 1 B 2 MET A 213 MET A 214 0 SHEET 2 B 2 THR A 233 ASN A 234 -1 O ASN A 234 N MET A 213 SSBOND 1 CYS A 135 CYS A 141 1555 1555 2.12 SSBOND 2 CYS A 173 CYS A 178 1555 1555 2.16 SITE 1 AC1 2 ASN A 234 GLN A 238 SITE 1 AC2 2 LYS A 47 TYR A 384 SITE 1 AC3 9 TRP A 97 SER A 136 LYS A 152 ALA A 155 SITE 2 AC3 9 GLU A 156 GLN A 159 HOH A 686 HOH A 699 SITE 3 AC3 9 HOH A 701 CRYST1 180.044 180.044 64.470 90.00 90.00 120.00 P 31 2 1 6 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 0.005554 0.003207 0.000000 0.00000 SCALE2 0.000000 0.006413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015511 0.00000