HEADER CELL INVASION 09-NOV-09 3KM5 TITLE CRYSTAL STRUCTURE ANALYSIS OF THE K2 CLEAVED ADHESIN DOMAIN OF LYS- TITLE 2 GINGIPAIN (KGP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE SPECIFIC CYSTEINE PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: K2 CLEAVED ADHESIN DOMAIN, RESIDUES 1157-1334; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS; SOURCE 3 ORGANISM_TAXID: 242619; SOURCE 4 STRAIN: W83; SOURCE 5 GENE: KGP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32 KEYWDS BETA JELLY ROLL BARREL, CLEAVED ADHESIN FAMILY, LYS-GINGIPAIN, KEYWDS 2 HEMAGGLUTINATION DOMAIN, CELL INVASION EXPDTA X-RAY DIFFRACTION AUTHOR N.LI,C.A.COLLYER,N.HUNTER REVDAT 4 20-MAR-24 3KM5 1 REMARK SEQADV LINK REVDAT 3 01-NOV-17 3KM5 1 REMARK REVDAT 2 26-MAY-10 3KM5 1 JRNL REVDAT 1 31-MAR-10 3KM5 0 JRNL AUTH N.LI,P.YUN,M.A.NADKARNI,N.B.GHADIKOLAEE,K.-A.NGUYEN,M.LEE, JRNL AUTH 2 N.HUNTER,C.A.COLLYER JRNL TITL STRUCTURE DETERMINATION AND ANALYSIS OF A HAEMOLYTIC JRNL TITL 2 GINGIPAIN ADHESIN DOMAIN FROM PORPHYROMONAS GINGIVALIS JRNL REF MOL.MICROBIOL. V. 76 861 2010 JRNL REFN ISSN 0950-382X JRNL PMID 20233299 JRNL DOI 10.1111/J.1365-2958.2010.07123.X REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0063 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 56068 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2829 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3876 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 183 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2646 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 304 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.67000 REMARK 3 B22 (A**2) : 0.79000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.041 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2756 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1726 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3764 ; 1.492 ; 1.924 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4209 ; 0.867 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 359 ; 7.915 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;32.258 ;24.754 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 378 ;11.145 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;13.482 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 406 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3186 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 586 ; 0.001 ; 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): 1749 ; 1.773 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 732 ; 0.601 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2778 ; 2.461 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1007 ; 2.979 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 981 ; 4.016 ; 6.000 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 : BABINET MODEL WITH 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 ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 3KM5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056164. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-08; 24-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON; APS REMARK 200 BEAMLINE : MX1; 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95667; 0.97949, 0.97962, REMARK 200 0.94947 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R; MARMOSAIC 300 REMARK 200 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56082 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 17.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8000 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) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.26600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, 0.2M AMMONIUM REMARK 280 NITRATE, 0.1M NA CITRATE, PH 5.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.92900 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 1334 REMARK 465 GLY B 1155 REMARK 465 SER B 1156 REMARK 465 ALA B 1287 REMARK 465 ASN B 1288 REMARK 465 GLY B 1289 REMARK 465 GLY B 1333 REMARK 465 GLY B 1334 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 ASP A1196 CG OD1 OD2 REMARK 470 ILE A1274 CG1 CG2 CD1 REMARK 470 ASN A1275 CG OD1 ND2 REMARK 470 LYS A1276 CD CE NZ REMARK 470 SER A1284 OG REMARK 470 THR A1285 CG2 REMARK 470 GLU A1286 CG CD OE1 OE2 REMARK 470 ASN A1288 CG OD1 ND2 REMARK 470 GLN A1293 CG CD OE1 NE2 REMARK 470 GLY A1333 C O REMARK 470 ASP B1196 CG OD1 OD2 REMARK 470 ILE B1274 CG1 CG2 CD1 REMARK 470 ASN B1275 CG OD1 ND2 REMARK 470 LYS B1276 CG CD CE NZ REMARK 470 THR B1285 CG2 REMARK 470 GLU B1286 CG CD OE1 OE2 REMARK 470 GLN B1293 CG CD OE1 NE2 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 ASN A1213 81.77 -153.99 REMARK 500 THR A1256 -85.08 -134.13 REMARK 500 LEU A1320 -105.87 -102.88 REMARK 500 ASN A1321 -76.83 -147.05 REMARK 500 MET A1332 64.46 -104.11 REMARK 500 THR B1256 -88.89 -133.94 REMARK 500 SER B1284 28.72 -140.64 REMARK 500 LEU B1320 -107.72 -96.99 REMARK 500 ASN B1321 -74.12 -148.53 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 A2011 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 3 O REMARK 620 2 ASP A1179 OD1 164.9 REMARK 620 3 ASP A1181 OD1 94.6 85.1 REMARK 620 4 ASP A1181 OD2 79.8 88.9 48.3 REMARK 620 5 ASP A1183 OD1 78.6 88.1 117.4 69.4 REMARK 620 6 GLN A1185 O 90.9 94.6 159.5 152.2 83.1 REMARK 620 7 ASN A1221 OD1 90.3 104.4 78.1 123.7 161.3 82.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A2012 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 8 O REMARK 620 2 THR A1162 O 89.8 REMARK 620 3 GLU A1164 OE2 100.7 81.1 REMARK 620 4 GLY A1202 O 76.4 150.8 76.5 REMARK 620 5 ASN A1205 O 171.2 91.4 88.1 106.2 REMARK 620 6 ASP A1326 OD1 84.9 74.6 155.1 128.3 87.0 REMARK 620 7 ASP A1326 OD2 92.9 125.1 150.7 81.8 79.3 51.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2012 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 2 O REMARK 620 2 THR B1162 O 91.1 REMARK 620 3 GLU B1164 OE2 98.3 79.5 REMARK 620 4 GLY B1202 O 74.9 150.4 77.0 REMARK 620 5 ASN B1205 O 174.8 91.8 86.5 104.3 REMARK 620 6 ASP B1326 OD1 89.8 75.9 154.2 128.8 86.8 REMARK 620 7 ASP B1326 OD2 96.8 127.2 149.0 81.0 78.0 52.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2011 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 116 O REMARK 620 2 ASP B1179 OD1 165.4 REMARK 620 3 ASP B1181 OD1 95.1 87.0 REMARK 620 4 ASP B1181 OD2 80.2 90.2 49.7 REMARK 620 5 ASP B1183 OD1 77.6 88.6 118.7 69.2 REMARK 620 6 GLN B1185 O 89.5 94.0 158.0 152.1 83.4 REMARK 620 7 ASN B1221 OD1 92.8 101.8 77.6 125.3 161.5 80.7 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 CA A 2011 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 2012 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2022 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 2021 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 2011 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 2012 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 2021 DBREF 3KM5 A 1157 1334 UNP O52050 O52050_PORGI 1157 1334 DBREF 3KM5 B 1157 1334 UNP O52050 O52050_PORGI 1157 1334 SEQADV 3KM5 GLY A 1155 UNP O52050 EXPRESSION TAG SEQADV 3KM5 SER A 1156 UNP O52050 EXPRESSION TAG SEQADV 3KM5 GLY B 1155 UNP O52050 EXPRESSION TAG SEQADV 3KM5 SER B 1156 UNP O52050 EXPRESSION TAG SEQRES 1 A 180 GLY SER ALA ASP PHE THR GLU THR PHE GLU SER SER THR SEQRES 2 A 180 HIS GLY GLU ALA PRO ALA GLU TRP THR THR ILE ASP ALA SEQRES 3 A 180 ASP GLY ASP GLY GLN GLY TRP LEU CYS LEU SER SER GLY SEQRES 4 A 180 GLN LEU ASP TRP LEU THR ALA HIS GLY GLY SER ASN VAL SEQRES 5 A 180 VAL SER SER PHE SER TRP ASN GLY MET ALA LEU ASN PRO SEQRES 6 A 180 ASP ASN TYR LEU ILE SER LYS ASP VAL THR GLY ALA THR SEQRES 7 A 180 LYS VAL LYS TYR TYR TYR ALA VAL ASN ASP GLY PHE PRO SEQRES 8 A 180 GLY ASP HIS TYR ALA VAL MET ILE SER LYS THR GLY THR SEQRES 9 A 180 ASN ALA GLY ASP PHE THR VAL VAL PHE GLU GLU THR PRO SEQRES 10 A 180 ASN GLY ILE ASN LYS GLY GLY ALA ARG PHE GLY LEU SER SEQRES 11 A 180 THR GLU ALA ASN GLY ALA LYS PRO GLN SER VAL TRP ILE SEQRES 12 A 180 GLU ARG THR VAL ASP LEU PRO ALA GLY THR LYS TYR VAL SEQRES 13 A 180 ALA PHE ARG HIS TYR ASN CYS SER ASP LEU ASN TYR ILE SEQRES 14 A 180 LEU LEU ASP ASP ILE GLN PHE THR MET GLY GLY SEQRES 1 B 180 GLY SER ALA ASP PHE THR GLU THR PHE GLU SER SER THR SEQRES 2 B 180 HIS GLY GLU ALA PRO ALA GLU TRP THR THR ILE ASP ALA SEQRES 3 B 180 ASP GLY ASP GLY GLN GLY TRP LEU CYS LEU SER SER GLY SEQRES 4 B 180 GLN LEU ASP TRP LEU THR ALA HIS GLY GLY SER ASN VAL SEQRES 5 B 180 VAL SER SER PHE SER TRP ASN GLY MET ALA LEU ASN PRO SEQRES 6 B 180 ASP ASN TYR LEU ILE SER LYS ASP VAL THR GLY ALA THR SEQRES 7 B 180 LYS VAL LYS TYR TYR TYR ALA VAL ASN ASP GLY PHE PRO SEQRES 8 B 180 GLY ASP HIS TYR ALA VAL MET ILE SER LYS THR GLY THR SEQRES 9 B 180 ASN ALA GLY ASP PHE THR VAL VAL PHE GLU GLU THR PRO SEQRES 10 B 180 ASN GLY ILE ASN LYS GLY GLY ALA ARG PHE GLY LEU SER SEQRES 11 B 180 THR GLU ALA ASN GLY ALA LYS PRO GLN SER VAL TRP ILE SEQRES 12 B 180 GLU ARG THR VAL ASP LEU PRO ALA GLY THR LYS TYR VAL SEQRES 13 B 180 ALA PHE ARG HIS TYR ASN CYS SER ASP LEU ASN TYR ILE SEQRES 14 B 180 LEU LEU ASP ASP ILE GLN PHE THR MET GLY GLY HET CA A2011 1 HET CA A2012 1 HET SO4 A2022 5 HET NO3 A2021 4 HET GOL B2001 6 HET CA B2011 1 HET CA B2012 1 HET NO3 B2021 4 HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM NO3 NITRATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CA 4(CA 2+) FORMUL 5 SO4 O4 S 2- FORMUL 6 NO3 2(N O3 1-) FORMUL 7 GOL C3 H8 O3 FORMUL 11 HOH *304(H2 O) HELIX 1 1 ASN A 1259 GLY A 1261 5 3 HELIX 2 2 ASN B 1259 GLY B 1261 5 3 SHEET 1 A 4 PHE A1159 GLU A1161 0 SHEET 2 A 4 TYR A1322 THR A1331 -1 O ILE A1328 N GLU A1161 SHEET 3 A 4 ASN A1205 PHE A1210 -1 N VAL A1207 O LEU A1325 SHEET 4 A 4 LEU A1188 SER A1191 -1 N LEU A1190 O VAL A1206 SHEET 1 B 4 PHE A1159 GLU A1161 0 SHEET 2 B 4 TYR A1322 THR A1331 -1 O ILE A1328 N GLU A1161 SHEET 3 B 4 LYS A1233 VAL A1240 -1 N LYS A1235 O GLN A1329 SHEET 4 B 4 ILE A1297 ASP A1302 -1 O VAL A1301 N VAL A1234 SHEET 1 C 5 THR A1176 ASP A1179 0 SHEET 2 C 5 ASP A1220 ILE A1224 -1 O ILE A1224 N THR A1176 SHEET 3 C 5 TYR A1309 TYR A1315 -1 O PHE A1312 N LEU A1223 SHEET 4 C 5 TYR A1249 SER A1254 -1 N MET A1252 O ALA A1311 SHEET 5 C 5 PHE A1263 GLU A1269 -1 O PHE A1267 N VAL A1251 SHEET 1 D 4 PHE B1159 GLU B1161 0 SHEET 2 D 4 TYR B1322 THR B1331 -1 O ILE B1328 N GLU B1161 SHEET 3 D 4 ASN B1205 PHE B1210 -1 N VAL B1207 O LEU B1325 SHEET 4 D 4 LEU B1188 SER B1191 -1 N LEU B1190 O VAL B1206 SHEET 1 E 4 PHE B1159 GLU B1161 0 SHEET 2 E 4 TYR B1322 THR B1331 -1 O ILE B1328 N GLU B1161 SHEET 3 E 4 LYS B1233 VAL B1240 -1 N LYS B1235 O GLN B1329 SHEET 4 E 4 ILE B1297 ASP B1302 -1 O VAL B1301 N VAL B1234 SHEET 1 F 5 THR B1176 ASP B1179 0 SHEET 2 F 5 ASP B1220 ILE B1224 -1 O ILE B1224 N THR B1176 SHEET 3 F 5 TYR B1309 TYR B1315 -1 O PHE B1312 N LEU B1223 SHEET 4 F 5 TYR B1249 SER B1254 -1 N MET B1252 O ALA B1311 SHEET 5 F 5 PHE B1263 GLU B1269 -1 O VAL B1266 N VAL B1251 LINK O HOH A 3 CA CA A2011 1555 1555 2.45 LINK O HOH A 8 CA CA A2012 1555 1555 2.36 LINK O THR A1162 CA CA A2012 1555 1555 2.43 LINK OE2 GLU A1164 CA CA A2012 1555 1555 2.37 LINK OD1 ASP A1179 CA CA A2011 1555 1555 2.29 LINK OD1 ASP A1181 CA CA A2011 1555 1555 2.42 LINK OD2 ASP A1181 CA CA A2011 1555 1555 2.81 LINK OD1 ASP A1183 CA CA A2011 1555 1555 2.40 LINK O GLN A1185 CA CA A2011 1555 1555 2.27 LINK O GLY A1202 CA CA A2012 1555 1555 2.47 LINK O ASN A1205 CA CA A2012 1555 1555 2.37 LINK OD1 ASN A1221 CA CA A2011 1555 1555 2.43 LINK OD1 ASP A1326 CA CA A2012 1555 1555 2.48 LINK OD2 ASP A1326 CA CA A2012 1555 1555 2.61 LINK O HOH B 2 CA CA B2012 1555 1555 2.38 LINK O HOH B 116 CA CA B2011 1555 1555 2.42 LINK O THR B1162 CA CA B2012 1555 1555 2.45 LINK OE2 GLU B1164 CA CA B2012 1555 1555 2.40 LINK OD1 ASP B1179 CA CA B2011 1555 1555 2.27 LINK OD1 ASP B1181 CA CA B2011 1555 1555 2.44 LINK OD2 ASP B1181 CA CA B2011 1555 1555 2.74 LINK OD1 ASP B1183 CA CA B2011 1555 1555 2.37 LINK O GLN B1185 CA CA B2011 1555 1555 2.24 LINK O GLY B1202 CA CA B2012 1555 1555 2.41 LINK O ASN B1205 CA CA B2012 1555 1555 2.35 LINK OD1 ASN B1221 CA CA B2011 1555 1555 2.43 LINK OD1 ASP B1326 CA CA B2012 1555 1555 2.43 LINK OD2 ASP B1326 CA CA B2012 1555 1555 2.64 SITE 1 AC1 6 HOH A 3 ASP A1179 ASP A1181 ASP A1183 SITE 2 AC1 6 GLN A1185 ASN A1221 SITE 1 AC2 6 HOH A 8 THR A1162 GLU A1164 GLY A1202 SITE 2 AC2 6 ASN A1205 ASP A1326 SITE 1 AC3 10 HOH A 52 HOH A 172 HOH A 259 HOH A 288 SITE 2 AC3 10 GLU A1161 THR A1162 PHE A1163 GLU A1164 SITE 3 AC3 10 SER A1165 ASN B1218 SITE 1 AC4 7 HOH A 304 GLY A1184 GLN A1185 GLY A1186 SITE 2 AC4 7 LEU A1188 ARG A1299 THR A1300 SITE 1 AC5 10 HOH B 58 TRP B1197 LEU B1198 THR B1199 SITE 2 AC5 10 ALA B1239 VAL B1240 GLN B1293 SER B1294 SITE 3 AC5 10 TRP B1296 TYR B1322 SITE 1 AC6 6 HOH B 116 ASP B1179 ASP B1181 ASP B1183 SITE 2 AC6 6 GLN B1185 ASN B1221 SITE 1 AC7 6 HOH B 2 THR B1162 GLU B1164 GLY B1202 SITE 2 AC7 6 ASN B1205 ASP B1326 SITE 1 AC8 9 HOH B 121 HOH B 237 GLY B1184 GLN B1185 SITE 2 AC8 9 GLY B1186 LEU B1188 GLU B1298 ARG B1299 SITE 3 AC8 9 THR B1300 CRYST1 29.911 59.858 85.672 90.00 94.23 90.00 P 1 21 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 0.033433 0.000000 0.002473 0.00000 SCALE2 0.000000 0.016706 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011704 0.00000