HEADER MEMBRANE PROTEIN 22-DEC-04 1YC9 TITLE THE CRYSTAL STRUCTURE OF THE OUTER MEMBRANE PROTEIN VCEC FROM THE TITLE 2 BACTERIAL PATHOGEN VIBRIO CHOLERAE AT 1.8 RESOLUTION CAVEAT 1YC9 BOG A 1001 HAS WRONG CHIRALITY AT ATOM C1 BOG A 1001 HAS CAVEAT 2 1YC9 WRONG CHIRALITY AT ATOM C3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTIDRUG RESISTANCE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VCEC; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 STRAIN: CVD101; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIBRIO CHOLERAE, OUTER MEMBRANE PROTEIN, MULTIDRUG RESISTANCE, KEYWDS 2 MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.FEDERICI,D.DU,F.WALAS,H.MATSUMURA,J.FERNANDEZ-RECIO,K.S.MCKEEGAN, AUTHOR 2 M.I.BORGES-WALMSLEY,B.F.LUISI,A.R.WALMSLEY REVDAT 7 29-MAY-24 1YC9 1 REMARK REVDAT 6 10-NOV-21 1YC9 1 REMARK SEQADV HETSYN REVDAT 5 29-JUL-20 1YC9 1 CAVEAT COMPND REMARK SEQADV REVDAT 5 2 1 HETNAM SITE REVDAT 4 13-JUL-11 1YC9 1 VERSN REVDAT 3 24-FEB-09 1YC9 1 VERSN REVDAT 2 19-APR-05 1YC9 1 JRNL REVDAT 1 01-MAR-05 1YC9 0 JRNL AUTH L.FEDERICI,D.DU,F.WALAS,H.MATSUMURA,J.FERNANDEZ-RECIO, JRNL AUTH 2 K.S.MCKEEGAN,M.I.BORGES-WALMSLEY,B.F.LUISI,A.R.WALMSLEY JRNL TITL THE CRYSTAL STRUCTURE OF THE OUTER MEMBRANE PROTEIN VCEC JRNL TITL 2 FROM THE BACTERIAL PATHOGEN VIBRIO CHOLERAE AT 1.8 A JRNL TITL 3 RESOLUTION JRNL REF J.BIOL.CHEM. V. 280 15307 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15684414 JRNL DOI 10.1074/JBC.M500401200 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 53358 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2708 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3703 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 175 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3125 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 315 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.80000 REMARK 3 B22 (A**2) : 1.80000 REMARK 3 B33 (A**2) : -2.70000 REMARK 3 B12 (A**2) : 0.90000 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): 0.107 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.508 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3201 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2899 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4361 ; 1.751 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6702 ; 1.055 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 419 ; 8.832 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 501 ; 0.254 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3680 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 647 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 762 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3320 ; 0.258 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1921 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 242 ; 0.236 ; 0.200 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): 22 ; 0.232 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 144 ; 0.302 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 43 ; 0.155 ; 0.200 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): 2048 ; 1.089 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3233 ; 1.939 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1153 ; 3.202 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1123 ; 5.175 ; 4.500 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 : 1.40 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 1YC9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031370. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53358 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 63.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 <I/SIGMA(I)> 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, TRIS, NACL, BETA-DDM, OCTYL-BETA REMARK 280 -GLUCOSIDE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 300 REMARK: BIOLOGICAL ASSEMBLY IS A TRIMER. REMARK 300 GENERATE CHAIN A BY ROTATING: REMARK 300 1.0 0.0 0.0 REMARK 300 0.0 1.0 0.0 REMARK 300 0.0 0.0 1.0 REMARK 300 AND TRANSLATING BY: REMARK 300 0.0 0.0 0.0 REMARK 300 GENERATE CHAIN B. ROTATE BY: REMARK 300 -0.5 -0.866 0.0 REMARK 300 0.866 -0.5 0.0 REMARK 300 0.0 0.0 1.0 REMARK 300 TRANSLATE BY: REMARK 300 1.0 1.0 0.0 REMARK 300 GENERATE CHAIN C. ROTATE BY: REMARK 300 -0.5 0.866 0.0 REMARK 300 -0.866 -0.5 0.0 REMARK 300 0.0 0.0 1.0 REMARK 300 TRANSLATE BY: REMARK 300 0.0 1.0 0.0 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 16410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 54750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -267.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 35.72900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 61.88444 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -35.72900 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 61.88444 REMARK 350 BIOMT3 3 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 MET A 43 REMARK 465 TRP A 44 REMARK 465 GLU A 45 REMARK 465 ALA A 46 REMARK 465 ASN A 47 REMARK 465 GLU A 48 REMARK 465 LEU A 49 REMARK 465 SER A 50 REMARK 465 SER A 51 REMARK 465 THR A 52 REMARK 465 ASN A 53 REMARK 465 THR A 54 REMARK 465 PHE A 55 REMARK 465 SER A 56 REMARK 465 HIS A 57 REMARK 465 GLN A 58 REMARK 465 ALA A 59 REMARK 465 GLU A 60 REMARK 465 MET A 61 REMARK 465 ASP A 62 REMARK 465 GLY A 288 REMARK 465 LEU A 289 REMARK 465 PRO A 290 REMARK 465 SER A 291 REMARK 465 GLU A 292 REMARK 465 ALA A 293 REMARK 465 GLY A 294 REMARK 465 THR A 481 REMARK 465 THR A 482 REMARK 465 GLU A 483 REMARK 465 SER A 484 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 GLU A 480 CG CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 86 CD OE1 NE2 REMARK 480 ARG A 97 CD NE CZ NH1 NH2 REMARK 480 LYS A 222 CG CD CE NZ REMARK 480 GLU A 277 CG CD OE1 OE2 REMARK 480 HIS A 300 CG ND1 CD2 CE1 NE2 REMARK 480 ARG A 308 NE CZ NH1 NH2 REMARK 480 GLN A 424 CD OE1 NE2 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 OE2 GLU A 229 OH TYR A 433 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 222 CB LYS A 222 CG -0.254 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 ASP A 74 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 112 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 115 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 303 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 351 CB - CG - OD1 ANGL. DEV. = 8.3 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 TYR A 131 -81.81 -139.52 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 ALA A 75 GLN A 76 145.30 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 HG A 1 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HG A 2 HG REMARK 620 2 CYS A 92 SG 90.0 REMARK 620 N 1 DBREF 1YC9 A 43 484 UNP Q9KS51 Q9KS51_VIBCH 43 484 SEQADV 1YC9 CYS A 92 UNP Q9KS51 GLU 92 ENGINEERED MUTATION SEQADV 1YC9 HIS A 396 UNP Q9KS51 TYR 396 CONFLICT SEQADV 1YC9 ILE A 398 UNP Q9KS51 VAL 398 CONFLICT SEQRES 1 A 442 MET TRP GLU ALA ASN GLU LEU SER SER THR ASN THR PHE SEQRES 2 A 442 SER HIS GLN ALA GLU MET ASP TRP PRO SER ALA ASN TRP SEQRES 3 A 442 TRP GLN ARG TYR GLN ASP ALA GLN LEU ASN HIS LEU ILE SEQRES 4 A 442 GLU GLU ALA LEU GLN HIS SER PRO SER LEU CYS MET ALA SEQRES 5 A 442 MET ALA ARG LEU LYS GLY ALA GLN GLY PHE ALA ARG GLN SEQRES 6 A 442 ALA GLY ALA ILE ARG SER PHE ASP LEU GLY LEU ALA ALA SEQRES 7 A 442 SER ALA THR GLU SER LYS VAL SER GLU ARG TYR GLN SER SEQRES 8 A 442 ALA THR PRO PRO ASP GLY TRP ASN ASP TYR GLY THR LEU SEQRES 9 A 442 THR LEU ASN PHE GLN TYR ASP PHE ASP PHE TRP GLY LYS SEQRES 10 A 442 ASN ARG ALA ALA VAL VAL ALA ALA THR SER GLU LEU ALA SEQRES 11 A 442 ALA ALA GLU ALA GLU SER VAL ALA ALA ARG LEU MET ILE SEQRES 12 A 442 SER THR SER ILE ALA ASN ALA TYR ALA GLU LEU ALA ARG SEQRES 13 A 442 LEU TYR ALA ASN GLN GLU THR VAL HIS ALA ALA LEU GLN SEQRES 14 A 442 VAL ARG ASN LYS THR VAL GLU LEU LEU GLU LYS ARG TYR SEQRES 15 A 442 ALA ASN GLY LEU GLU THR LEU GLY SER VAL SER GLN ALA SEQRES 16 A 442 LYS ALA VAL ALA ALA SER VAL GLU ALA GLU LEU LEU GLY SEQRES 17 A 442 ILE GLN GLU SER ILE GLN LEU GLN LYS ASN ALA LEU ALA SEQRES 18 A 442 ALA LEU VAL GLY GLN GLY PRO ASP ARG ALA ALA SER ILE SEQRES 19 A 442 GLU GLU PRO HIS ILE THR LEU THR SER ARG TYR GLY LEU SEQRES 20 A 442 PRO SER GLU ALA GLY VAL GLY LEU LEU GLY HIS ARG ALA SEQRES 21 A 442 ASP ILE THR ALA ALA ARG TRP ARG ALA GLU ALA ALA ALA SEQRES 22 A 442 GLN GLN VAL GLY ILE ALA GLN ALA GLN PHE TYR PRO ASP SEQRES 23 A 442 VAL THR LEU SER ALA PHE ILE GLY TYR GLN ALA PHE GLY SEQRES 24 A 442 LEU ASP HIS LEU PHE ASP SER GLY ASN ASP ALA GLY ALA SEQRES 25 A 442 ILE GLY PRO ALA ILE TYR LEU PRO LEU PHE THR GLY GLY SEQRES 26 A 442 ARG LEU GLU GLY GLN LEU THR SER ALA GLU ALA ARG TYR SEQRES 27 A 442 GLN GLU ALA VAL ALA GLN TYR ASN GLY THR LEU VAL GLN SEQRES 28 A 442 ALA LEU HIS GLU ILE ALA ASP VAL VAL THR SER SER GLN SEQRES 29 A 442 ALA LEU GLN ALA ARG ILE ASN LYS THR GLU GLN ALA VAL SEQRES 30 A 442 GLN GLN ALA GLU GLN ALA LEU HIS ILE ALA THR ASN ARG SEQRES 31 A 442 TYR GLN GLY GLY LEU ALA THR TYR LEU ASP VAL LEU VAL SEQRES 32 A 442 ALA GLU GLU SER LEU LEU ASN ASN GLN ARG ALA LEU VAL SEQRES 33 A 442 ASN LEU GLN SER ARG ALA PHE SER LEU ASP LEU ALA LEU SEQRES 34 A 442 ILE HIS ALA LEU GLY GLY GLY PHE GLU THR THR GLU SER HET BOG A1001 20 HET HG A 1 1 HET HG A 2 1 HETNAM BOG OCTYL BETA-D-GLUCOPYRANOSIDE HETNAM HG MERCURY (II) ION HETSYN BOG BETA-OCTYLGLUCOSIDE; OCTYL BETA-D-GLUCOSIDE; OCTYL D- HETSYN 2 BOG GLUCOSIDE; OCTYL GLUCOSIDE FORMUL 2 BOG C14 H28 O6 FORMUL 3 HG 2(HG 2+) FORMUL 5 HOH *315(H2 O) HELIX 1 1 ASN A 67 GLN A 73 5 7 HELIX 2 2 ASP A 74 HIS A 87 1 14 HELIX 3 3 SER A 88 ALA A 110 1 23 HELIX 4 4 ILE A 111 SER A 113 5 3 HELIX 5 5 GLY A 158 ASN A 226 1 69 HELIX 6 6 THR A 230 VAL A 266 1 37 HELIX 7 7 GLY A 269 ILE A 276 5 8 HELIX 8 8 VAL A 295 GLY A 299 5 5 HELIX 9 9 ARG A 301 GLN A 324 1 24 HELIX 10 10 LEU A 342 LEU A 345 5 4 HELIX 11 11 GLY A 367 GLN A 434 1 68 HELIX 12 12 THR A 439 GLY A 476 1 38 SHEET 1 A 4 ASP A 115 LYS A 126 0 SHEET 2 A 4 TRP A 140 ASP A 153 -1 O ASN A 149 N GLY A 117 SHEET 3 A 4 ASP A 328 PHE A 340 -1 O ILE A 335 N LEU A 148 SHEET 4 A 4 ASP A 351 TYR A 360 -1 O TYR A 360 N ASP A 328 LINK HG HG A 1 HG HG A 2 1555 1555 2.86 LINK HG HG A 1 SG CYS A 92 1555 1555 2.41 LINK HG HG A 2 O CYS A 92 1555 1555 3.03 CRYST1 71.458 71.458 190.702 90.00 90.00 120.00 P 3 2 1 6 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 0.013994 0.008080 0.000000 0.00000 SCALE2 0.000000 0.016159 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005244 0.00000