HEADER HYDROLASE 27-JUL-17 5OLJ TITLE CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS DIPEPTIDYL PEPTIDASE 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPEPTIDYL PEPTIDASE IV; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS; SOURCE 3 ORGANISM_TAXID: 837; SOURCE 4 GENE: DPPIV, PGN_1469; SOURCE 5 EXPRESSION_SYSTEM: PORPHYROMONAS GINGIVALIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 837 KEYWDS DIPEPTIDYL PEPTIDASE 4, PEPTIDASE INHIBITOR, PORPHYROMONAS KEYWDS 2 GINGIVALIS, BIOFILM, DIPEPTIDYL PEPTIDASE 9, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.FULOP REVDAT 3 17-JAN-24 5OLJ 1 REMARK REVDAT 2 16-OCT-19 5OLJ 1 REMARK REVDAT 1 06-SEP-17 5OLJ 0 JRNL AUTH D.REA,R.VAN ELZEN,H.DE WINTER,S.VAN GOETHEM,B.LANDUYT, JRNL AUTH 2 W.LUYTEN,L.SCHOOFS,P.VAN DER VEKEN,K.AUGUSTYNS,I.DE MEESTER, JRNL AUTH 3 V.FULOP,A.M.LAMBEIR JRNL TITL CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS DIPEPTIDYL JRNL TITL 2 PEPTIDASE 4 AND STRUCTURE-ACTIVITY RELATIONSHIPS BASED ON JRNL TITL 3 INHIBITOR PROFILING. JRNL REF EUR J MED CHEM V. 139 482 2017 JRNL REFN ISSN 1768-3254 JRNL PMID 28826083 JRNL DOI 10.1016/J.EJMECH.2017.08.024 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.REA,A.M.LAMBEIR,Y.KUMAGAI,I.DE MEESTER,S.SCHARPE,V.FULOP REMARK 1 TITL EXPRESSION, PURIFICATION AND PRELIMINARY CRYSTALLOGRAPHIC REMARK 1 TITL 2 ANALYSIS OF DIPEPTIDYL PEPTIDASE IV FROM PORPHYROMONAS REMARK 1 TITL 3 GINGIVALIS. REMARK 1 REF ACTA CRYSTALLOGR. D BIOL. V. 60 1871 2004 REMARK 1 REF 2 CRYSTALLOGR. REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 15388936 REMARK 1 DOI 10.1107/S0907444904017639 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 46837 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1974 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) : 3288 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.5290 REMARK 3 BIN FREE R VALUE SET COUNT : 137 REMARK 3 BIN FREE R VALUE : 0.5310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5631 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 398 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.75000 REMARK 3 B22 (A**2) : -0.75000 REMARK 3 B33 (A**2) : 1.50000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.258 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.204 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.784 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.839 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.810 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5774 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5334 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7826 ; 1.634 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12236 ; 0.812 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 702 ; 7.154 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 284 ;33.536 ;23.380 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 948 ;16.061 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;21.102 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 834 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6608 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1422 ; 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): 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): 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 21 A 43 REMARK 3 ORIGIN FOR THE GROUP (A): 49.6962 37.1992 16.0372 REMARK 3 T TENSOR REMARK 3 T11: 0.0749 T22: 0.1115 REMARK 3 T33: 0.0090 T12: -0.0342 REMARK 3 T13: 0.0210 T23: -0.0210 REMARK 3 L TENSOR REMARK 3 L11: 9.1110 L22: 3.0108 REMARK 3 L33: 3.7690 L12: -3.5623 REMARK 3 L13: 2.8972 L23: -1.8613 REMARK 3 S TENSOR REMARK 3 S11: 0.1437 S12: 0.6439 S13: -0.0122 REMARK 3 S21: -0.0539 S22: -0.0832 S23: 0.0101 REMARK 3 S31: -0.3074 S32: 0.2134 S33: -0.0604 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 44 A 80 REMARK 3 ORIGIN FOR THE GROUP (A): 25.1933 43.3797 2.3556 REMARK 3 T TENSOR REMARK 3 T11: 0.0539 T22: 0.0457 REMARK 3 T33: 0.0175 T12: -0.0309 REMARK 3 T13: -0.0163 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 1.4082 L22: 4.4739 REMARK 3 L33: 1.3677 L12: 1.9872 REMARK 3 L13: -0.8439 L23: 0.0065 REMARK 3 S TENSOR REMARK 3 S11: 0.0798 S12: -0.0116 S13: -0.0667 REMARK 3 S21: -0.0004 S22: -0.0781 S23: -0.1508 REMARK 3 S31: -0.1127 S32: -0.0493 S33: -0.0017 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 81 A 321 REMARK 3 ORIGIN FOR THE GROUP (A): 19.2924 58.1134 22.9238 REMARK 3 T TENSOR REMARK 3 T11: 0.0532 T22: 0.0368 REMARK 3 T33: 0.0282 T12: 0.0094 REMARK 3 T13: -0.0135 T23: -0.0125 REMARK 3 L TENSOR REMARK 3 L11: 0.2653 L22: 0.2512 REMARK 3 L33: 0.3427 L12: 0.1042 REMARK 3 L13: 0.0076 L23: -0.0449 REMARK 3 S TENSOR REMARK 3 S11: -0.0330 S12: -0.0023 S13: 0.0395 REMARK 3 S21: -0.0361 S22: -0.0018 S23: 0.0503 REMARK 3 S31: -0.0395 S32: -0.0624 S33: 0.0348 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 322 A 723 REMARK 3 ORIGIN FOR THE GROUP (A): 36.3683 35.0938 32.7516 REMARK 3 T TENSOR REMARK 3 T11: 0.0625 T22: 0.0304 REMARK 3 T33: 0.0095 T12: -0.0004 REMARK 3 T13: -0.0173 T23: -0.0098 REMARK 3 L TENSOR REMARK 3 L11: 0.2874 L22: 0.2356 REMARK 3 L33: 0.2898 L12: 0.1178 REMARK 3 L13: 0.1027 L23: 0.0851 REMARK 3 S TENSOR REMARK 3 S11: 0.0101 S12: 0.0131 S13: -0.0157 REMARK 3 S21: 0.0322 S22: 0.0085 S23: -0.0034 REMARK 3 S31: 0.0413 S32: 0.0066 S33: -0.0186 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5OLJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200006012. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : XENOCS GENIX 3D CU HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48811 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5KBY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (W/V) PEG 8000, 20% (V/V) ETHYLENE REMARK 280 GLYCOL, 0.02 M SODIUM L-GLUTAMATE, 0.02 M DL-ALANINE, 0.02 M REMARK 280 GLYCINE, 0.02 M DL-LYSINE, 0.02 M DLSERINE, AND 0.1 M BICINE/ REMARK 280 TRIS PH 8.5, VAPOR DIFFUSION, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 78.90500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 54.55000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 54.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.45250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 54.55000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 54.55000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 118.35750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 54.55000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.55000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.45250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 54.55000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.55000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 118.35750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 78.90500 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: 300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1101 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1170 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 ARG A 3 REMARK 465 PRO A 4 REMARK 465 VAL A 5 REMARK 465 ILE A 6 REMARK 465 ILE A 7 REMARK 465 LEU A 8 REMARK 465 LEU A 9 REMARK 465 LEU A 10 REMARK 465 GLY A 11 REMARK 465 ILE A 12 REMARK 465 VAL A 13 REMARK 465 THR A 14 REMARK 465 MET A 15 REMARK 465 CYS A 16 REMARK 465 ALA A 17 REMARK 465 MET A 18 REMARK 465 ALA A 19 REMARK 465 GLN A 20 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 NZ LYS A 376 O HOH A 901 2.08 REMARK 500 SD MET A 559 O HOH A 1252 2.15 REMARK 500 OD2 ASP A 238 O HOH A 902 2.19 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 83 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 83 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 MET A 227 CG - SD - CE ANGL. DEV. = -11.0 DEGREES REMARK 500 ARG A 280 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ASP A 499 CB - CG - OD2 ANGL. DEV. = -5.5 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 SER A 40 -165.77 -122.48 REMARK 500 ARG A 43 83.74 -57.73 REMARK 500 ILE A 113 -74.07 -102.53 REMARK 500 TYR A 114 -154.05 -122.60 REMARK 500 ASN A 182 19.80 54.88 REMARK 500 SER A 183 -67.38 -145.95 REMARK 500 ARG A 324 -64.61 -107.78 REMARK 500 THR A 478 -170.34 -170.33 REMARK 500 ALA A 485 43.75 73.77 REMARK 500 ASP A 497 59.11 -101.39 REMARK 500 SER A 512 -5.12 81.71 REMARK 500 GLN A 560 51.91 -155.35 REMARK 500 SER A 593 -123.13 70.61 REMARK 500 ALA A 617 52.73 37.35 REMARK 500 ARG A 635 -167.92 56.64 REMARK 500 ASN A 640 49.91 -147.60 REMARK 500 ASN A 670 -65.42 -103.68 REMARK 500 ASP A 697 19.93 56.53 REMARK 500 ILE A 702 76.57 33.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 43 GLY A 44 141.12 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 A1298 DISTANCE = 7.01 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 801 DBREF 5OLJ A 1 723 UNP B2RKU3 B2RKU3_PORG3 1 723 SEQRES 1 A 723 MET LYS ARG PRO VAL ILE ILE LEU LEU LEU GLY ILE VAL SEQRES 2 A 723 THR MET CYS ALA MET ALA GLN THR GLY ASP LYS PRO VAL SEQRES 3 A 723 ASP LEU LYS GLU ILE THR SER GLY MET PHE TYR ALA ARG SEQRES 4 A 723 SER ALA GLY ARG GLY ILE ARG SER MET PRO ASP GLY GLU SEQRES 5 A 723 HIS TYR THR GLU MET ASN ARG GLU ARG THR ALA ILE VAL SEQRES 6 A 723 ARG TYR ASN TYR ALA SER GLY LYS ALA VAL ASP THR LEU SEQRES 7 A 723 PHE SER ILE GLU ARG ALA ARG GLU CYS PRO PHE LYS GLN SEQRES 8 A 723 ILE GLN ASN TYR GLU VAL SER SER THR GLY HIS HIS ILE SEQRES 9 A 723 LEU LEU PHE THR ASP MET GLU SER ILE TYR ARG HIS SER SEQRES 10 A 723 TYR ARG ALA ALA VAL TYR ASP TYR ASP VAL ARG ARG ASN SEQRES 11 A 723 LEU VAL LYS PRO LEU SER GLU HIS VAL GLY LYS VAL MET SEQRES 12 A 723 ILE PRO THR PHE SER PRO ASP GLY ARG MET VAL ALA PHE SEQRES 13 A 723 VAL ARG ASP ASN ASN ILE PHE ILE LYS LYS PHE ASP PHE SEQRES 14 A 723 ASP THR GLU VAL GLN VAL THR THR ASP GLY GLN ILE ASN SEQRES 15 A 723 SER VAL LEU ASN GLY ALA THR ASP TRP VAL TYR GLU GLU SEQRES 16 A 723 GLU PHE GLY VAL THR ASN LEU MET SER TRP SER ALA ASP SEQRES 17 A 723 ASN ALA PHE LEU ALA PHE VAL ARG SER ASP GLU SER ALA SEQRES 18 A 723 VAL PRO GLU TYR ARG MET PRO MET TYR GLU ASP LYS LEU SEQRES 19 A 723 TYR PRO GLU ASP TYR THR TYR LYS TYR PRO LYS ALA GLY SEQRES 20 A 723 GLU LYS ASN SER THR VAL SER LEU HIS LEU TYR ASN VAL SEQRES 21 A 723 ALA ASP ARG ASN THR LYS SER VAL SER LEU PRO ILE ASP SEQRES 22 A 723 ALA ASP GLY TYR ILE PRO ARG ILE ALA PHE THR ASP ASN SEQRES 23 A 723 ALA ASP GLU LEU ALA VAL MET THR LEU ASN ARG LEU GLN SEQRES 24 A 723 ASN ASP PHE LYS MET TYR TYR VAL HIS PRO LYS SER LEU SEQRES 25 A 723 VAL PRO LYS LEU ILE LEU GLN ASP MET ASN LYS ARG TYR SEQRES 26 A 723 VAL ASP SER ASP TRP ILE GLN ALA LEU LYS PHE THR ALA SEQRES 27 A 723 GLY GLY GLY PHE ALA TYR VAL SER GLU LYS ASP GLY PHE SEQRES 28 A 723 ALA HIS ILE TYR LEU TYR ASP ASN LYS GLY VAL MET HIS SEQRES 29 A 723 ARG ARG ILE THR SER GLY ASN TRP ASP VAL THR LYS LEU SEQRES 30 A 723 TYR GLY VAL ASP ALA SER GLY THR VAL PHE TYR GLN SER SEQRES 31 A 723 ALA GLU GLU SER PRO ILE ARG ARG ALA VAL TYR ALA ILE SEQRES 32 A 723 ASP ALA LYS GLY ARG LYS THR LYS LEU SER LEU ASN VAL SEQRES 33 A 723 GLY THR ASN ASP ALA LEU PHE SER GLY ASN TYR ALA TYR SEQRES 34 A 723 TYR ILE ASN THR TYR SER SER ALA ALA THR PRO THR VAL SEQRES 35 A 723 VAL SER VAL PHE ARG SER LYS GLY ALA LYS GLU LEU ARG SEQRES 36 A 723 THR LEU GLU ASP ASN VAL ALA LEU ARG GLU ARG LEU LYS SEQRES 37 A 723 ALA TYR ARG TYR ASN PRO LYS GLU PHE THR ILE ILE LYS SEQRES 38 A 723 THR GLN SER ALA LEU GLU LEU ASN ALA TRP ILE VAL LYS SEQRES 39 A 723 PRO ILE ASP PHE ASP PRO SER ARG HIS TYR PRO VAL LEU SEQRES 40 A 723 MET VAL GLN TYR SER GLY PRO ASN SER GLN GLN VAL LEU SEQRES 41 A 723 ASP ARG TYR SER PHE ASP TRP GLU HIS TYR LEU ALA SER SEQRES 42 A 723 LYS GLY TYR VAL VAL ALA CYS VAL ASP GLY ARG GLY THR SEQRES 43 A 723 GLY ALA ARG GLY GLU GLU TRP ARG LYS CYS THR TYR MET SEQRES 44 A 723 GLN LEU GLY VAL PHE GLU SER ASP ASP GLN ILE ALA ALA SEQRES 45 A 723 ALA THR ALA ILE GLY GLN LEU PRO TYR VAL ASP ALA ALA SEQRES 46 A 723 ARG ILE GLY ILE TRP GLY TRP SER TYR GLY GLY TYR THR SEQRES 47 A 723 THR LEU MET SER LEU CYS ARG GLY ASN GLY THR PHE LYS SEQRES 48 A 723 ALA GLY ILE ALA VAL ALA PRO VAL ALA ASP TRP ARG PHE SEQRES 49 A 723 TYR ASP SER VAL TYR THR GLU ARG PHE MET ARG THR PRO SEQRES 50 A 723 LYS GLU ASN ALA SER GLY TYR LYS MET SER SER ALA LEU SEQRES 51 A 723 ASP VAL ALA SER GLN LEU GLN GLY ASN LEU LEU ILE VAL SEQRES 52 A 723 SER GLY SER ALA ASP ASP ASN VAL HIS LEU GLN ASN THR SEQRES 53 A 723 MET LEU PHE THR GLU ALA LEU VAL GLN ALA ASN ILE PRO SEQRES 54 A 723 PHE ASP MET ALA ILE TYR MET ASP LYS ASN HIS SER ILE SEQRES 55 A 723 TYR GLY GLY ASN THR ARG TYR HIS LEU TYR THR ARG LYS SEQRES 56 A 723 ALA LYS PHE LEU PHE ASP ASN LEU HET GOL A 801 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *398(H2 O) HELIX 1 AA1 ASP A 27 SER A 33 1 7 HELIX 2 AA2 ASP A 190 GLY A 198 1 9 HELIX 3 AA3 ASP A 327 ALA A 333 1 7 HELIX 4 AA4 ASN A 460 TYR A 470 1 11 HELIX 5 AA5 TRP A 527 SER A 533 1 7 HELIX 6 AA6 GLY A 550 CYS A 556 1 7 HELIX 7 AA7 GLY A 562 GLY A 577 1 16 HELIX 8 AA8 SER A 593 GLY A 606 1 14 HELIX 9 AA9 ASP A 621 TYR A 625 5 5 HELIX 10 AB1 ASP A 626 ARG A 635 1 10 HELIX 11 AB2 ASN A 640 SER A 647 1 8 HELIX 12 AB3 ALA A 649 LEU A 656 5 8 HELIX 13 AB4 HIS A 672 ALA A 686 1 15 HELIX 14 AB5 ASN A 706 LEU A 723 1 18 SHEET 1 AA1 4 ARG A 46 SER A 47 0 SHEET 2 AA1 4 HIS A 53 MET A 57 -1 O THR A 55 N ARG A 46 SHEET 3 AA1 4 ALA A 63 ASN A 68 -1 O TYR A 67 N TYR A 54 SHEET 4 AA1 4 ALA A 74 SER A 80 -1 O ASP A 76 N ARG A 66 SHEET 1 AA2 4 ASN A 94 VAL A 97 0 SHEET 2 AA2 4 HIS A 103 SER A 112 -1 O PHE A 107 N ASN A 94 SHEET 3 AA2 4 TYR A 118 ASP A 126 -1 O TYR A 123 N LEU A 106 SHEET 4 AA2 4 LEU A 131 PRO A 134 -1 O LEU A 131 N ASP A 126 SHEET 1 AA3 4 MET A 143 PHE A 147 0 SHEET 2 AA3 4 MET A 153 ARG A 158 -1 O ALA A 155 N THR A 146 SHEET 3 AA3 4 ASN A 161 LYS A 166 -1 O LYS A 165 N VAL A 154 SHEET 4 AA3 4 THR A 171 GLN A 174 -1 O THR A 171 N LYS A 166 SHEET 1 AA4 3 VAL A 184 ASN A 186 0 SHEET 2 AA4 3 PHE A 211 ASP A 218 -1 O SER A 217 N LEU A 185 SHEET 3 AA4 3 MET A 203 TRP A 205 -1 N SER A 204 O ALA A 213 SHEET 1 AA5 4 VAL A 184 ASN A 186 0 SHEET 2 AA5 4 PHE A 211 ASP A 218 -1 O SER A 217 N LEU A 185 SHEET 3 AA5 4 THR A 252 ASN A 259 -1 O SER A 254 N ARG A 216 SHEET 4 AA5 4 ASN A 264 VAL A 268 -1 O VAL A 268 N LEU A 255 SHEET 1 AA6 2 GLU A 224 MET A 229 0 SHEET 2 AA6 2 GLU A 237 LYS A 242 -1 O TYR A 239 N MET A 227 SHEET 1 AA7 4 TYR A 277 PHE A 283 0 SHEET 2 AA7 4 LEU A 290 LEU A 295 -1 O LEU A 295 N TYR A 277 SHEET 3 AA7 4 ASP A 301 VAL A 307 -1 O TYR A 305 N VAL A 292 SHEET 4 AA7 4 PRO A 314 MET A 321 -1 O ILE A 317 N MET A 304 SHEET 1 AA8 4 LYS A 335 PHE A 336 0 SHEET 2 AA8 4 PHE A 342 SER A 346 -1 O ALA A 343 N LYS A 335 SHEET 3 AA8 4 HIS A 353 TYR A 357 -1 O TYR A 355 N TYR A 344 SHEET 4 AA8 4 MET A 363 ARG A 366 -1 O ARG A 365 N LEU A 356 SHEET 1 AA9 4 VAL A 374 VAL A 380 0 SHEET 2 AA9 4 VAL A 386 SER A 390 -1 O PHE A 387 N GLY A 379 SHEET 3 AA9 4 ALA A 399 ILE A 403 -1 O TYR A 401 N TYR A 388 SHEET 4 AA9 4 LYS A 409 LYS A 411 -1 O THR A 410 N ALA A 402 SHEET 1 AB1 4 THR A 418 PHE A 423 0 SHEET 2 AB1 4 TYR A 429 SER A 435 -1 O THR A 433 N ASP A 420 SHEET 3 AB1 4 VAL A 442 ARG A 447 -1 O PHE A 446 N TYR A 430 SHEET 4 AB1 4 LYS A 452 GLU A 458 -1 O LEU A 454 N VAL A 445 SHEET 1 AB2 8 GLU A 476 LYS A 481 0 SHEET 2 AB2 8 GLU A 487 VAL A 493 -1 O ILE A 492 N GLU A 476 SHEET 3 AB2 8 VAL A 537 VAL A 541 -1 O VAL A 538 N VAL A 493 SHEET 4 AB2 8 TYR A 504 VAL A 509 1 N PRO A 505 O VAL A 537 SHEET 5 AB2 8 VAL A 582 TRP A 592 1 O ASP A 583 N TYR A 504 SHEET 6 AB2 8 ALA A 612 VAL A 616 1 O VAL A 616 N GLY A 591 SHEET 7 AB2 8 ASN A 659 GLY A 665 1 O ASN A 659 N GLY A 613 SHEET 8 AB2 8 ASP A 691 TYR A 695 1 O ASP A 691 N LEU A 660 SITE 1 AC1 4 TYR A 511 SER A 593 TYR A 594 TYR A 625 CRYST1 109.100 109.100 157.810 90.00 90.00 90.00 P 41 21 2 8 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 0.009166 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009166 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006337 0.00000