HEADER HYDROLASE 17-MAR-15 4YTB TITLE CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE TITLE 2 DEIMINASE (PPAD) IN COMPLEX WITH DIPEPTIDE ASP-GLN. 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.- SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS; SOURCE 3 ORGANISM_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 4 10-JAN-24 4YTB 1 LINK REVDAT 3 07-MAR-18 4YTB 1 SOURCE REMARK LINK SITE REVDAT 3 2 1 ATOM REVDAT 2 15-JUL-15 4YTB 1 JRNL REVDAT 1 01-JUL-15 4YTB 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. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 90283 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.000 REMARK 3 FREE R VALUE TEST SET COUNT : 903 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.61 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 6269 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1567 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6204 REMARK 3 BIN R VALUE (WORKING SET) : 0.1565 REMARK 3 BIN FREE R VALUE : 0.1816 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 1.04 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 65 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 : 3330 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 688 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.07820 REMARK 3 B22 (A**2) : -1.99880 REMARK 3 B33 (A**2) : -0.07940 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.115 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.053 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.048 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.049 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.045 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 : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3574 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4878 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1628 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 99 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 531 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3574 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 465 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 15 ; 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 : 4908 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.05 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 5.06 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.65 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 - 465 A|999 - 999} REMARK 3 ORIGIN FOR THE GROUP (A): -13.8039 13.4579 -10.2203 REMARK 3 T TENSOR REMARK 3 T11: -0.0054 T22: 0.0029 REMARK 3 T33: -0.0086 T12: -0.0009 REMARK 3 T13: -0.0004 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.2273 L22: 0.3665 REMARK 3 L33: 0.2555 L12: -0.0468 REMARK 3 L13: -0.0375 L23: 0.0158 REMARK 3 S TENSOR REMARK 3 S11: 0.0119 S12: 0.0186 S13: -0.0009 REMARK 3 S21: -0.0285 S22: -0.0039 S23: 0.0246 REMARK 3 S31: 0.0024 S32: 0.0063 S33: -0.0080 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|502 - 503} REMARK 3 ORIGIN FOR THE GROUP (A): -12.2874 -7.4049 -5.8598 REMARK 3 T TENSOR REMARK 3 T11: 0.0168 T22: -0.0096 REMARK 3 T33: 0.0038 T12: 0.0163 REMARK 3 T13: 0.0020 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.2947 L22: 0.0425 REMARK 3 L33: 0.0679 L12: 0.0784 REMARK 3 L13: 0.0512 L23: -0.1055 REMARK 3 S TENSOR REMARK 3 S11: -0.0011 S12: 0.0096 S13: -0.0147 REMARK 3 S21: 0.0019 S22: -0.0099 S23: 0.0250 REMARK 3 S31: 0.0623 S32: 0.0032 S33: 0.0110 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4YTB 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_1000208078. 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 : 5.5-6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 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 : 90283 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 46.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 0.30500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.500 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 (%): 47.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRI-SODIUM CITRATE, 2M AMMONIUM REMARK 280 SULFATE, PH5.5-6.5, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K 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 30.26700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.83200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.65300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.83200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.26700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.65300 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: 1940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 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: 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 C ASP A 502 N GLN A 503 1.33 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 THR A 140 -53.49 71.40 REMARK 500 ASN A 151 38.60 -80.62 REMARK 500 TRP A 240 -14.03 -143.18 REMARK 500 ASN A 291 61.02 -154.81 REMARK 500 ASN A 302 -122.67 54.59 REMARK 500 ASN A 310 23.64 -140.44 REMARK 500 ASP A 347 101.70 -162.38 REMARK 500 ALA A 348 -142.26 -139.15 REMARK 500 SER A 393 127.59 -170.13 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 TYR A 243 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1285 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A1286 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A1287 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A1288 DISTANCE = 6.35 ANGSTROMS 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 ASP A 502 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 82.5 REMARK 620 3 ASP A 158 O 105.2 165.2 REMARK 620 4 ASP A 158 OD1 164.5 87.7 82.0 REMARK 620 5 HOH A 806 O 79.5 100.7 69.1 90.6 REMARK 620 6 HOH A 890 O 94.6 91.7 100.1 97.6 165.5 REMARK 620 N 1 2 3 4 5 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 ASP A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GLN 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AZI A 514 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YT9 RELATED DB: PDB DBREF 4YTB A 44 475 UNP Q9RQJ2 PAD_PORGI 44 475 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 CYS 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 ASP A 502 8 HET GLN A 503 10 HET GOL A 504 6 HET GOL A 505 6 HET GOL A 506 12 HET PO4 A 507 5 HET PO4 A 508 5 HET PO4 A 509 5 HET PO4 A 510 5 HET PO4 A 511 5 HET IMD A 512 5 HET CL A 513 1 HET AZI A 514 3 HETNAM NA SODIUM ION HETNAM ASP ASPARTIC ACID HETNAM GLN GLUTAMINE HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETNAM IMD IMIDAZOLE HETNAM CL CHLORIDE ION HETNAM AZI AZIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NA NA 1+ FORMUL 3 ASP C4 H7 N O4 FORMUL 4 GLN C5 H10 N2 O3 FORMUL 5 GOL 3(C3 H8 O3) FORMUL 8 PO4 5(O4 P 3-) FORMUL 13 IMD C3 H5 N2 1+ FORMUL 14 CL CL 1- FORMUL 15 AZI N3 1- FORMUL 16 HOH *688(H2 O) HELIX 1 AA1 PRO A 76 ASP A 87 1 12 HELIX 2 AA2 SER A 95 GLY A 110 1 16 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 PHE A 160 1 7 HELIX 6 AA6 PHE A 160 GLY A 169 1 10 HELIX 7 AA7 THR A 180 TYR A 184 5 5 HELIX 8 AA8 HIS A 196 GLU A 201 1 6 HELIX 9 AA9 SER A 206 GLY A 219 1 14 HELIX 10 AB1 HIS A 236 CYS A 239 5 4 HELIX 11 AB2 GLN A 260 ALA A 273 1 14 HELIX 12 AB3 PRO A 312 MET A 327 1 16 HELIX 13 AB4 LEU A 349 THR A 353 5 5 SHEET 1 AA1 4 VAL A 55 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 MET A 172 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 VAL A 89 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 251 SHEET 1 AA5 3 LEU A 299 LEU A 301 0 SHEET 2 AA5 3 ARG A 304 VAL A 309 -1 O ARG A 304 N LEU A 301 SHEET 3 AA5 3 GLU A 331 LYS A 336 1 O ILE A 333 N VAL A 305 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 SER A 416 O HIS A 419 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 GLN A 373 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 ALA A 410 N CYS A 397 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 GLN A 373 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 GLU A 447 N ALA A 439 LINK OD1 ASP A 147 NA NA A 501 1555 1555 2.44 LINK O PHE A 148 NA NA A 501 1555 1555 2.30 LINK O ASP A 158 NA NA A 501 1555 1555 2.41 LINK OD1 ASP A 158 NA NA A 501 1555 1555 2.38 LINK NA NA A 501 O HOH A 806 1555 1555 2.63 LINK NA NA A 501 O HOH A 890 1555 1555 2.37 CISPEP 1 GLY A 53 PRO A 54 0 -2.66 CISPEP 2 TYR A 71 PRO A 72 0 -5.48 CISPEP 3 GLY A 311 PRO A 312 0 0.38 CISPEP 4 GLY A 375 PRO A 376 0 3.49 CISPEP 5 SER A 393 PRO A 394 0 -10.14 CISPEP 6 TYR A 449 PRO A 450 0 1.46 SITE 1 AC1 5 ASP A 147 PHE A 148 ASP A 158 HOH A 806 SITE 2 AC1 5 HOH A 890 SITE 1 AC2 6 TRP A 127 ARG A 154 TYR A 233 GLN A 503 SITE 2 AC2 6 HOH A 796 HOH A 970 SITE 1 AC3 14 TRP A 127 ASP A 130 ARG A 152 ARG A 154 SITE 2 AC3 14 TYR A 233 ILE A 234 THR A 346 ASP A 347 SITE 3 AC3 14 CYS A 351 ASP A 502 HOH A 613 HOH A 634 SITE 4 AC3 14 HOH A 825 HOH A 970 SITE 1 AC4 10 ASP A 266 MET A 267 TYR A 270 PRO A 455 SITE 2 AC4 10 HOH A 633 HOH A 703 HOH A 716 HOH A 792 SITE 3 AC4 10 HOH A 842 HOH A 949 SITE 1 AC5 8 LYS A 176 ASN A 202 SER A 204 HOH A 673 SITE 2 AC5 8 HOH A 692 HOH A 741 HOH A 751 HOH A 872 SITE 1 AC6 16 SER A 206 GLN A 207 ALA A 208 GLU A 283 SITE 2 AC6 16 LYS A 459 HOH A 605 HOH A 649 HOH A 679 SITE 3 AC6 16 HOH A 699 HOH A 709 HOH A 745 HOH A 761 SITE 4 AC6 16 HOH A 794 HOH A 963 HOH A1066 HOH A1122 SITE 1 AC7 4 ALA A 390 THR A 391 ASN A 442 HOH A 721 SITE 1 AC8 8 PRO A 76 MET A 77 ALA A 338 HOH A 615 SITE 2 AC8 8 HOH A 638 HOH A 684 HOH A 697 HOH A 947 SITE 1 AC9 4 GLN A 212 LYS A 215 HOH A 710 HOH A 757 SITE 1 AD1 5 THR A 280 LYS A 281 HOH A 606 HOH A 620 SITE 2 AD1 5 HOH A 785 SITE 1 AD2 3 ASN A 428 LYS A 429 GLU A 465 SITE 1 AD3 2 ARG A 70 PRO A 72 SITE 1 AD4 8 HIS A 196 TYR A 199 VAL A 225 PRO A 455 SITE 2 AD4 8 HOH A 603 HOH A 625 HOH A 917 HOH A 955 CRYST1 60.534 71.306 105.664 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 0.016520 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009464 0.00000