HEADER HYDROLASE 17-MAR-15 4YTG TITLE CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE TITLE 2 DEIMINASE (PPAD) MUTANT C351A IN COMPLEX WITH DIPEPTIDE MET-ARG. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYLARGININE DEIMINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 44-475; COMPND 5 EC: 3.5.3.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS (STRAIN ATCC BAA-308 / SOURCE 3 W83); SOURCE 4 ORGANISM_TAXID: 242619; SOURCE 5 GENE: PG_1424; SOURCE 6 EXPRESSION_SYSTEM: PORPHYROMONAS GINGIVALIS W83; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 242619 KEYWDS PEPTIDYLARGININE DEIMINASE, CITRULLINATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.GOULAS,D.MIZGALSKA,I.GARCIA-FERRER,T.KANTYKA,T.GUEVARA, AUTHOR 2 B.SZMIGIELSKI,A.SROKA,C.MILLAN,I.USON,F.VEILLARD,B.POTEMPA,P.MYDEL, AUTHOR 3 M.SOLA,J.POTEMPA,F.X.GOMIS-RUTH REVDAT 5 10-JAN-24 4YTG 1 REMARK REVDAT 4 26-SEP-18 4YTG 1 COMPND SOURCE REVDAT 3 28-SEP-16 4YTG 1 REVDAT 2 15-JUL-15 4YTG 1 JRNL REVDAT 1 01-JUL-15 4YTG 0 JRNL AUTH T.GOULAS,D.MIZGALSKA,I.GARCIA-FERRER,T.KANTYKA,T.GUEVARA, JRNL AUTH 2 B.SZMIGIELSKI,A.SROKA,C.MILLAN,I.USON,F.VEILLARD,B.POTEMPA, JRNL AUTH 3 P.MYDEL,M.SOLA,J.POTEMPA,F.X.GOMIS-RUTH JRNL TITL STRUCTURE AND MECHANISM OF A BACTERIAL HOST-PROTEIN JRNL TITL 2 CITRULLINATING VIRULENCE FACTOR, PORPHYROMONAS GINGIVALIS JRNL TITL 3 PEPTIDYLARGININE DEIMINASE. JRNL REF SCI REP V. 5 11969 2015 JRNL REFN ESSN 2045-2322 JRNL PMID 26132828 JRNL DOI 10.1038/SREP11969 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 38882 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.800 REMARK 3 FREE R VALUE TEST SET COUNT : 699 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 19 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.85 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.69 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2992 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2233 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2940 REMARK 3 BIN R VALUE (WORKING SET) : 0.2226 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 1.74 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 52 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3296 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 426 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.50060 REMARK 3 B22 (A**2) : -0.55160 REMARK 3 B33 (A**2) : -2.94900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 7.12600 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.192 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.118 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.105 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.112 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.102 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3453 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4686 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1551 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 94 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 496 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3453 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 447 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 3 ; 1.000 ; HARMONIC REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4393 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.99 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.07 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.56 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|44 - 463 A|998 - 999} REMARK 3 ORIGIN FOR THE GROUP (A): 45.0393 49.7269 86.4719 REMARK 3 T TENSOR REMARK 3 T11: -0.0334 T22: -0.0322 REMARK 3 T33: -0.0107 T12: 0.0232 REMARK 3 T13: -0.0059 T23: -0.0155 REMARK 3 L TENSOR REMARK 3 L11: 0.8336 L22: 0.5818 REMARK 3 L33: 1.0653 L12: -0.1070 REMARK 3 L13: 0.7100 L23: -0.2101 REMARK 3 S TENSOR REMARK 3 S11: 0.0384 S12: 0.0062 S13: -0.0129 REMARK 3 S21: -0.0228 S22: -0.0776 S23: 0.0301 REMARK 3 S31: -0.0391 S32: -0.0619 S33: 0.0393 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {L|1 - 2} REMARK 3 ORIGIN FOR THE GROUP (A): 55.7333 36.0163 96.7573 REMARK 3 T TENSOR REMARK 3 T11: 0.0182 T22: -0.0309 REMARK 3 T33: 0.0129 T12: 0.0190 REMARK 3 T13: -0.0497 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 0.2016 L22: 0.0000 REMARK 3 L33: -0.0528 L12: -0.0692 REMARK 3 L13: 0.0092 L23: 0.0556 REMARK 3 S TENSOR REMARK 3 S11: 0.0026 S12: 0.0079 S13: -0.0198 REMARK 3 S21: 0.0235 S22: 0.0017 S23: -0.0129 REMARK 3 S31: 0.0239 S32: -0.0080 S33: -0.0043 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4YTG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208083. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5-6.4 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38882 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 67.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.52900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4YT9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRI-SODIUM CITRATE, 20% [W/V] REMARK 280 POLYETHYLENE GLYCOL 3,000, PH5.5-6.5, PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 52.68000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.66000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.68000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.66000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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 ALA A 374 REMARK 465 GLY A 375 REMARK 465 PRO A 376 REMARK 465 ASN A 464 REMARK 465 GLU A 465 REMARK 465 THR A 466 REMARK 465 ASN A 467 REMARK 465 THR A 468 REMARK 465 CYS A 469 REMARK 465 THR A 470 REMARK 465 VAL A 471 REMARK 465 THR A 472 REMARK 465 GLY A 473 REMARK 465 ALA A 474 REMARK 465 ALA A 475 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 THR A 140 -48.74 55.90 REMARK 500 ASN A 151 36.88 -77.84 REMARK 500 TRP A 240 -15.25 -144.27 REMARK 500 ASN A 291 60.26 -150.51 REMARK 500 ASN A 302 -118.17 56.80 REMARK 500 ASP A 347 100.11 -164.83 REMARK 500 ALA A 348 -139.48 -137.52 REMARK 500 SER A 393 133.19 -171.73 REMARK 500 ASN A 430 -2.30 79.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 MET A 503 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 NA A 501 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 147 OD1 REMARK 620 2 PHE A 148 O 81.5 REMARK 620 3 ASP A 158 O 105.4 154.3 REMARK 620 4 ASP A 158 OD1 158.4 85.7 79.5 REMARK 620 5 HOH A 797 O 96.1 95.7 107.9 102.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CYS A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MET A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ARG 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AZI A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AZI A 512 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YT9 RELATED DB: PDB DBREF 4YTG A 44 475 UNP Q9RQJ2 PAD_PORGI 44 475 SEQADV 4YTG ALA A 351 UNP Q9RQJ2 CYS 351 ENGINEERED MUTATION SEQRES 1 A 432 ALA PHE GLN GLU THR ASN PRO PRO ALA GLY PRO VAL ARG SEQRES 2 A 432 ALA ILE ALA GLU TYR GLU ARG SER ALA ALA VAL LEU VAL SEQRES 3 A 432 ARG TYR PRO PHE GLY ILE PRO MET GLU LEU ILE LYS GLU SEQRES 4 A 432 LEU ALA LYS ASN ASP LYS VAL ILE THR ILE VAL ALA SER SEQRES 5 A 432 GLU SER GLN LYS ASN THR VAL ILE THR GLN TYR THR GLN SEQRES 6 A 432 SER GLY VAL ASN LEU SER ASN CYS ASP PHE ILE ILE ALA SEQRES 7 A 432 LYS THR ASP SER TYR TRP THR ARG ASP TYR THR GLY TRP SEQRES 8 A 432 PHE ALA MET TYR ASP THR ASN LYS VAL GLY LEU VAL ASP SEQRES 9 A 432 PHE ILE TYR ASN ARG PRO ARG PRO ASN ASP ASP GLU PHE SEQRES 10 A 432 PRO LYS TYR GLU ALA GLN TYR LEU GLY ILE GLU MET PHE SEQRES 11 A 432 GLY MET LYS LEU LYS GLN THR GLY GLY ASN TYR MET THR SEQRES 12 A 432 ASP GLY TYR GLY SER ALA VAL GLN SER HIS ILE ALA TYR SEQRES 13 A 432 THR GLU ASN SER SER LEU SER GLN ALA GLN VAL ASN GLN SEQRES 14 A 432 LYS MET LYS ASP TYR LEU GLY ILE THR HIS HIS ASP VAL SEQRES 15 A 432 VAL GLN ASP PRO ASN GLY GLU TYR ILE ASN HIS VAL ASP SEQRES 16 A 432 CYS TRP GLY LYS TYR LEU ALA PRO ASN LYS ILE LEU ILE SEQRES 17 A 432 ARG LYS VAL PRO ASP ASN HIS PRO GLN HIS GLN ALA LEU SEQRES 18 A 432 GLU ASP MET ALA ALA TYR PHE ALA ALA GLN THR CYS ALA SEQRES 19 A 432 TRP GLY THR LYS TYR GLU VAL TYR ARG ALA LEU ALA THR SEQRES 20 A 432 ASN GLU GLN PRO TYR THR ASN SER LEU ILE LEU ASN ASN SEQRES 21 A 432 ARG VAL PHE VAL PRO VAL ASN GLY PRO ALA SER VAL ASP SEQRES 22 A 432 ASN ASP ALA LEU ASN VAL TYR LYS THR ALA MET PRO GLY SEQRES 23 A 432 TYR GLU ILE ILE GLY VAL LYS GLY ALA SER GLY THR PRO SEQRES 24 A 432 TRP LEU GLY THR ASP ALA LEU HIS ALA ARG THR HIS GLU SEQRES 25 A 432 VAL ALA ASP LYS GLY TYR LEU TYR ILE LYS HIS TYR PRO SEQRES 26 A 432 ILE LEU GLY GLU GLN ALA GLY PRO ASP TYR LYS ILE GLU SEQRES 27 A 432 ALA ASP VAL VAL SER CYS ALA ASN ALA THR ILE SER PRO SEQRES 28 A 432 VAL GLN CYS TYR TYR ARG ILE ASN GLY SER GLY SER PHE SEQRES 29 A 432 LYS ALA ALA ASP MET THR MET GLU SER THR GLY HIS TYR SEQRES 30 A 432 THR TYR SER PHE THR GLY LEU ASN LYS ASN ASP LYS VAL SEQRES 31 A 432 GLU TYR TYR ILE SER ALA ALA ASP ASN SER GLY ARG LYS SEQRES 32 A 432 GLU THR TYR PRO PHE ILE GLY GLU PRO ASP PRO PHE LYS SEQRES 33 A 432 PHE THR CYS MET ASN GLU THR ASN THR CYS THR VAL THR SEQRES 34 A 432 GLY ALA ALA HET NA A 501 1 HET CYS A 502 7 HET MET A 503 8 HET ARG A 504 12 HET GOL A 505 6 HET GOL A 506 6 HET GOL A 507 6 HET GOL A 508 6 HET GOL A 509 6 HET CL A 510 1 HET AZI A 511 3 HET AZI A 512 3 HETNAM NA SODIUM ION HETNAM CYS CYSTEINE HETNAM MET METHIONINE HETNAM ARG ARGININE HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM AZI AZIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NA NA 1+ FORMUL 3 CYS C3 H7 N O2 S FORMUL 4 MET C5 H11 N O2 S FORMUL 5 ARG C6 H15 N4 O2 1+ FORMUL 6 GOL 5(C3 H8 O3) FORMUL 11 CL CL 1- FORMUL 12 AZI 2(N3 1-) FORMUL 14 HOH *426(H2 O) HELIX 1 AA1 PRO A 76 ASP A 87 1 12 HELIX 2 AA2 SER A 95 SER A 109 1 15 HELIX 3 AA3 ASN A 112 SER A 114 5 3 HELIX 4 AA4 TRP A 127 THR A 132 1 6 HELIX 5 AA5 ARG A 154 GLY A 169 1 16 HELIX 6 AA6 THR A 180 TYR A 184 5 5 HELIX 7 AA7 HIS A 196 GLU A 201 1 6 HELIX 8 AA8 SER A 206 GLY A 219 1 14 HELIX 9 AA9 HIS A 236 CYS A 239 5 4 HELIX 10 AB1 GLN A 260 ALA A 273 1 14 HELIX 11 AB2 PRO A 312 MET A 327 1 16 HELIX 12 AB3 LEU A 349 THR A 353 5 5 SHEET 1 AA1 4 ARG A 56 ALA A 57 0 SHEET 2 AA1 4 TRP A 134 TYR A 138 -1 O MET A 137 N ARG A 56 SHEET 3 AA1 4 LYS A 142 TYR A 150 -1 O GLY A 144 N ALA A 136 SHEET 4 AA1 4 GLU A 171 GLN A 179 1 O PHE A 173 N ASP A 147 SHEET 1 AA2 4 CYS A 116 ILE A 120 0 SHEET 2 AA2 4 LYS A 88 VAL A 93 1 N THR A 91 O ASP A 117 SHEET 3 AA2 4 SER A 64 ARG A 70 1 N VAL A 67 O ILE A 90 SHEET 4 AA2 4 HIS A 354 ALA A 357 -1 O HIS A 354 N LEU A 68 SHEET 1 AA3 3 MET A 185 THR A 186 0 SHEET 2 AA3 3 SER A 191 SER A 195 -1 O VAL A 193 N MET A 185 SHEET 3 AA3 3 HIS A 222 VAL A 226 1 O ASP A 224 N ALA A 192 SHEET 1 AA4 3 GLY A 241 ALA A 245 0 SHEET 2 AA4 3 LYS A 248 LYS A 253 -1 O LEU A 250 N LYS A 242 SHEET 3 AA4 3 GLU A 283 LEU A 288 1 O TYR A 285 N ILE A 249 SHEET 1 AA5 3 LEU A 299 LEU A 301 0 SHEET 2 AA5 3 ARG A 304 VAL A 309 -1 O PHE A 306 N LEU A 299 SHEET 3 AA5 3 GLU A 331 LYS A 336 1 O VAL A 335 N VAL A 307 SHEET 1 AA6 4 LEU A 362 HIS A 366 0 SHEET 2 AA6 4 LYS A 379 SER A 386 -1 O ASP A 383 N LYS A 365 SHEET 3 AA6 4 HIS A 419 SER A 423 -1 O TYR A 420 N ALA A 382 SHEET 4 AA6 4 THR A 413 SER A 416 -1 N THR A 413 O THR A 421 SHEET 1 AA7 5 GLY A 371 GLN A 373 0 SHEET 2 AA7 5 PHE A 458 CYS A 462 1 O THR A 461 N GLY A 371 SHEET 3 AA7 5 LYS A 432 ASP A 441 -1 N VAL A 433 O PHE A 460 SHEET 4 AA7 5 ILE A 392 ILE A 401 -1 N GLN A 396 O SER A 438 SHEET 5 AA7 5 LYS A 408 ASP A 411 -1 O LYS A 408 N TYR A 399 SHEET 1 AA8 4 GLY A 371 GLN A 373 0 SHEET 2 AA8 4 PHE A 458 CYS A 462 1 O THR A 461 N GLY A 371 SHEET 3 AA8 4 LYS A 432 ASP A 441 -1 N VAL A 433 O PHE A 460 SHEET 4 AA8 4 LYS A 446 TYR A 449 -1 O TYR A 449 N ILE A 437 SSBOND 1 CYS A 462 CYS A 502 1555 1555 2.03 LINK OD1 ASP A 147 NA NA A 501 1555 1555 2.46 LINK O PHE A 148 NA NA A 501 1555 1555 2.34 LINK O ASP A 158 NA NA A 501 1555 1555 2.38 LINK OD1 ASP A 158 NA NA A 501 1555 1555 2.36 LINK NA NA A 501 O HOH A 797 1555 1555 2.34 CISPEP 1 GLY A 53 PRO A 54 0 -3.39 CISPEP 2 TYR A 71 PRO A 72 0 -7.20 CISPEP 3 GLY A 311 PRO A 312 0 -2.57 CISPEP 4 SER A 393 PRO A 394 0 -4.20 CISPEP 5 TYR A 449 PRO A 450 0 5.39 SITE 1 AC1 4 ASP A 147 PHE A 148 ASP A 158 HOH A 797 SITE 1 AC2 7 TYR A 378 PHE A 424 THR A 425 GLY A 426 SITE 2 AC2 7 LEU A 427 PHE A 460 CYS A 462 SITE 1 AC3 5 TRP A 127 ARG A 154 TYR A 233 ARG A 504 SITE 2 AC3 5 HOH A 724 SITE 1 AC4 14 TRP A 127 ASP A 130 ARG A 152 ARG A 154 SITE 2 AC4 14 GLY A 182 TYR A 233 ILE A 234 HIS A 236 SITE 3 AC4 14 ASP A 238 THR A 346 ALA A 351 MET A 503 SITE 4 AC4 14 HOH A 764 HOH A 914 SITE 1 AC5 7 ILE A 149 LYS A 176 ASN A 202 SER A 204 SITE 2 AC5 7 HOH A 798 HOH A 804 HOH A 824 SITE 1 AC6 5 ASP A 266 TYR A 270 HOH A 631 HOH A 740 SITE 2 AC6 5 HOH A1001 SITE 1 AC7 8 VAL A 55 ARG A 56 GLY A 219 LYS A 365 SITE 2 AC7 8 TYR A 367 HOH A 643 HOH A 771 HOH A 904 SITE 1 AC8 8 ASN A 247 LYS A 248 GLU A 283 PRO A 450 SITE 2 AC8 8 ASP A 456 AZI A 512 HOH A 815 HOH A 869 SITE 1 AC9 7 TYR A 399 TYR A 422 SER A 423 PHE A 424 SITE 2 AC9 7 THR A 425 LEU A 427 HOH A 674 SITE 1 AD1 1 ASN A 49 SITE 1 AD2 4 GLU A 232 ASN A 235 HOH A 604 HOH A 678 SITE 1 AD3 5 LYS A 248 GLU A 283 TYR A 285 ASP A 456 SITE 2 AD3 5 GOL A 508 CRYST1 105.360 59.320 84.610 90.00 126.59 90.00 C 1 2 1 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 0.009491 0.000000 0.007046 0.00000 SCALE2 0.000000 0.016858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014720 0.00000