HEADER HYDROLASE 17-MAR-15 4YT9 TITLE CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE TITLE 2 DEIMINASE (PPAD) SUBSTRATE-UNBOUND. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYLARGININE DEIMINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 44-475; COMPND 5 EC: 3.5.3.- SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS W83; 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 1 15-JUL-15 4YT9 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. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.5 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 64233 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.200 REMARK 3 FREE R VALUE TEST SET COUNT : 772 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.54 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.52 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 4344 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1792 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4289 REMARK 3 BIN R VALUE (WORKING SET) : 0.1783 REMARK 3 BIN FREE R VALUE : 0.2469 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 1.27 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 55 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 : 3349 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.29400 REMARK 3 B22 (A**2) : 2.79450 REMARK 3 B33 (A**2) : -0.50050 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) : 0.158 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.071 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.068 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.067 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.066 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 : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3513 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4766 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1580 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 94 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 510 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3513 ; 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 : 451 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : 6 ; 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 : 4572 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.03 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.50 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.67 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|44 - 70 A|125 - 359 A|996 - 999} REMARK 3 ORIGIN FOR THE GROUP (A): 19.8658 35.1583 37.4495 REMARK 3 T TENSOR REMARK 3 T11: -0.0347 T22: -0.0376 REMARK 3 T33: -0.0313 T12: 0.0072 REMARK 3 T13: 0.0064 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.4687 L22: 0.9799 REMARK 3 L33: 0.3974 L12: -0.0117 REMARK 3 L13: 0.0114 L23: 0.0242 REMARK 3 S TENSOR REMARK 3 S11: -0.0095 S12: -0.0728 S13: 0.0058 REMARK 3 S21: 0.0679 S22: -0.0010 S23: 0.1272 REMARK 3 S31: -0.0237 S32: -0.0839 S33: 0.0105 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|71 - 124} REMARK 3 ORIGIN FOR THE GROUP (A): 14.0604 18.5860 51.9995 REMARK 3 T TENSOR REMARK 3 T11: 0.0123 T22: -0.0010 REMARK 3 T33: -0.0350 T12: -0.0173 REMARK 3 T13: 0.0839 T23: 0.0652 REMARK 3 L TENSOR REMARK 3 L11: 0.8076 L22: 2.7458 REMARK 3 L33: 0.3003 L12: -0.1951 REMARK 3 L13: 0.5890 L23: -0.2787 REMARK 3 S TENSOR REMARK 3 S11: -0.0313 S12: -0.1957 S13: -0.1550 REMARK 3 S21: 0.3172 S22: 0.1160 S23: 0.2974 REMARK 3 S31: 0.0472 S32: -0.1590 S33: -0.0848 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|360 - 464 A|995 - 995} REMARK 3 ORIGIN FOR THE GROUP (A): 47.7072 30.8412 38.8953 REMARK 3 T TENSOR REMARK 3 T11: -0.0565 T22: -0.0155 REMARK 3 T33: -0.0227 T12: -0.0277 REMARK 3 T13: -0.0226 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.2007 L22: 0.7904 REMARK 3 L33: 2.9768 L12: -0.1703 REMARK 3 L13: -0.9392 L23: 0.5056 REMARK 3 S TENSOR REMARK 3 S11: 0.0727 S12: -0.1377 S13: -0.1431 REMARK 3 S21: 0.0201 S22: 0.0266 S23: -0.1682 REMARK 3 S31: -0.1276 S32: 0.3717 S33: -0.0994 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4YT9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208068. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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) : 0.9786 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 : 64233 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 42.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.19000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: BAR SHAPED. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM ACETATE (PH4.5), 25% REMARK 280 [W/V] POLYETHYLENE GLYCOL 3350, 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 29.28000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.84000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.84000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.28000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.15000 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 TOTAL BURIED SURFACE AREA: 1860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 -55.95 66.29 REMARK 500 ASN A 141 45.07 -140.77 REMARK 500 ASN A 291 55.11 -154.00 REMARK 500 ASN A 302 -120.15 56.01 REMARK 500 ALA A 348 -141.72 -138.81 REMARK 500 TYR A 378 55.42 -91.63 REMARK 500 SER A 393 127.73 -179.45 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 A1042 DISTANCE = 5.86 ANGSTROMS 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 81.2 REMARK 620 3 ASP A 158 O 105.0 164.7 REMARK 620 4 ASP A 158 OD1 160.7 88.8 81.0 REMARK 620 5 HOH A 818 O 93.6 95.3 98.2 103.8 REMARK 620 6 HOH A 860 O 82.4 98.8 68.7 82.8 164.5 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 GOL 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 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 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 DBREF 4YT9 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 4GJ 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 4GJ 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 4GJ MET ASN GLU THR ASN THR CYS THR VAL THR SEQRES 34 A 432 GLY ALA ALA MODRES 4YT9 4GJ A 239 CYS MODIFIED RESIDUE MODRES 4YT9 4GJ A 351 CYS MODIFIED RESIDUE MODRES 4YT9 4GJ A 462 CYS MODIFIED RESIDUE HET 4GJ A 239 13 HET CSO A 239 7 HET 4GJ A 351 13 HET 4GJ A 462 13 HET NA A 501 1 HET GOL A 502 6 HET GOL A 503 6 HET GOL A 504 6 HET GOL A 505 6 HET GOL A 506 6 HET GOL A 507 6 HET GOL A 508 6 HETNAM 4GJ 3-(PYRIDIN-4-YLDISULFANYL)-L-ALANINE HETNAM CSO S-HYDROXYCYSTEINE HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 4GJ 3(C8 H10 N2 O2 S2) FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 NA NA 1+ FORMUL 3 GOL 7(C3 H8 O3) FORMUL 10 HOH *460(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 4GJ 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 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 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 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 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 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 422 N ILE A 380 SHEET 4 AA6 4 THR A 413 SER A 416 -1 N THR A 413 O THR A 421 SHEET 1 AA7 4 LYS A 408 ASP A 411 0 SHEET 2 AA7 4 ILE A 392 ILE A 401 -1 N TYR A 399 O LYS A 408 SHEET 3 AA7 4 LYS A 432 ASP A 441 -1 O SER A 438 N GLN A 396 SHEET 4 AA7 4 LYS A 446 TYR A 449 -1 O TYR A 449 N ILE A 437 SHEET 1 AA8 4 LYS A 408 ASP A 411 0 SHEET 2 AA8 4 ILE A 392 ILE A 401 -1 N TYR A 399 O LYS A 408 SHEET 3 AA8 4 LYS A 432 ASP A 441 -1 O SER A 438 N GLN A 396 SHEET 4 AA8 4 PHE A 458 THR A 461 -1 O PHE A 460 N VAL A 433 LINK OD1 ASP A 147 NA NA A 501 1555 1555 2.47 LINK O PHE A 148 NA NA A 501 1555 1555 2.38 LINK O ASP A 158 NA NA A 501 1555 1555 2.37 LINK OD1 ASP A 158 NA NA A 501 1555 1555 2.35 LINK C ASP A 238 N A4GJ A 239 1555 1555 1.33 LINK C ASP A 238 N BCSO A 239 1555 1555 1.33 LINK C A4GJ A 239 N TRP A 240 1555 1555 1.36 LINK C BCSO A 239 N TRP A 240 1555 1555 1.36 LINK C HIS A 350 N 4GJ A 351 1555 1555 1.33 LINK C 4GJ A 351 N ARG A 352 1555 1555 1.34 LINK C THR A 461 N 4GJ A 462 1555 1555 1.34 LINK C 4GJ A 462 N MET A 463 1555 1555 1.33 LINK NA NA A 501 O HOH A 818 1555 1555 2.40 LINK NA NA A 501 O HOH A 860 1555 1555 2.57 CISPEP 1 GLY A 53 PRO A 54 0 -7.87 CISPEP 2 TYR A 71 PRO A 72 0 -3.96 CISPEP 3 GLY A 311 PRO A 312 0 -2.75 CISPEP 4 GLY A 375 PRO A 376 0 1.98 CISPEP 5 SER A 393 PRO A 394 0 -2.53 CISPEP 6 TYR A 449 PRO A 450 0 8.18 SITE 1 AC1 5 ASP A 147 PHE A 148 ASP A 158 HOH A 818 SITE 2 AC1 5 HOH A 860 SITE 1 AC2 11 HIS A 196 TYR A 199 GLN A 207 VAL A 225 SITE 2 AC2 11 VAL A 226 GLN A 227 PRO A 328 PRO A 455 SITE 3 AC2 11 ASP A 456 HOH A 614 HOH A 618 SITE 1 AC3 9 VAL A 226 GLN A 227 ASP A 266 PRO A 455 SITE 2 AC3 9 HOH A 605 HOH A 620 HOH A 641 HOH A 643 SITE 3 AC3 9 HOH A 853 SITE 1 AC4 7 ILE A 149 LYS A 176 ASN A 202 SER A 204 SITE 2 AC4 7 HOH A 819 HOH A 857 HOH A 863 SITE 1 AC5 6 PRO A 54 ARG A 56 TYR A 138 THR A 140 SITE 2 AC5 6 TYR A 363 HOH A1026 SITE 1 AC6 11 LYS A 248 TRP A 278 PRO A 450 ASP A 456 SITE 2 AC6 11 PRO A 457 LYS A 459 HOH A 836 HOH A 914 SITE 3 AC6 11 HOH A 915 HOH A 916 HOH A1007 SITE 1 AC7 5 VAL A 284 TYR A 285 HOH A 631 HOH A 654 SITE 2 AC7 5 HOH A 927 SITE 1 AC8 7 ASP A 228 ASN A 235 TRP A 240 ALA A 263 SITE 2 AC8 7 LEU A 264 MET A 267 HOH A 788 CRYST1 58.560 60.300 113.680 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 0.017077 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016584 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008797 0.00000