HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 28-OCT-04 1XVS TITLE CRYSTAL STRUCTURE OF APAG PROTEIN FROM VIBRIO CHOLERAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN APAG; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: APAG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS APAG, MCSG APC26324, MIDWEST CENTER FOR STRUCTURAL GENOMICS, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, PSI, STRUCTURAL GENOMICS, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR C.CHANG,A.JOACHIMIAK,H.LI,MIDWEST CENTER FOR STRUCTURAL GENOMICS AUTHOR 2 (MCSG) REVDAT 7 15-NOV-23 1XVS 1 REMARK REVDAT 6 23-AUG-23 1XVS 1 REMARK SEQADV LINK REVDAT 5 13-JUL-11 1XVS 1 VERSN REVDAT 4 24-FEB-09 1XVS 1 VERSN REVDAT 3 21-JUN-05 1XVS 1 JRNL REVDAT 2 18-JAN-05 1XVS 1 REMARK REVDAT 1 14-DEC-04 1XVS 0 JRNL AUTH C.CHANG,A.JOACHIMIAK,H.LI,S.MOY, JRNL AUTH 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) JRNL TITL CRYSTAL STRUCTURE OF APAG FROM VIBRIO CHOLERAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 17250 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 931 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) : 2.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 935 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1972 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 248 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.21000 REMARK 3 B22 (A**2) : -2.22000 REMARK 3 B33 (A**2) : 2.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.77000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.194 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.200 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.153 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.769 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2013 ; 0.038 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2731 ; 2.749 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 246 ; 7.360 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;34.697 ;25.102 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 350 ;18.698 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;25.197 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 310 ; 0.212 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1524 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 938 ; 0.284 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1369 ; 0.329 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 209 ; 0.229 ; 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): 61 ; 0.226 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.213 ; 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): 1280 ; 1.790 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2018 ; 2.558 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 844 ; 5.093 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 713 ; 7.326 ; 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 : 2 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 1 A 124 REMARK 3 ORIGIN FOR THE GROUP (A): 23.5770 0.8730 1.3780 REMARK 3 T TENSOR REMARK 3 T11: 0.0727 T22: -0.0090 REMARK 3 T33: 0.0269 T12: 0.0045 REMARK 3 T13: 0.0728 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.2741 L22: 1.2741 REMARK 3 L33: 1.4625 L12: 0.2395 REMARK 3 L13: -0.6209 L23: -0.7871 REMARK 3 S TENSOR REMARK 3 S11: 0.0164 S12: -0.0333 S13: 0.0473 REMARK 3 S21: -0.1175 S22: 0.0284 S23: -0.1215 REMARK 3 S31: 0.0958 S32: -0.0168 S33: -0.0447 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 : B 1 B 124 REMARK 3 ORIGIN FOR THE GROUP (A): 2.7380 2.4890 24.8800 REMARK 3 T TENSOR REMARK 3 T11: -0.0165 T22: 0.0195 REMARK 3 T33: 0.0128 T12: -0.0081 REMARK 3 T13: 0.0053 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 1.3723 L22: 1.3035 REMARK 3 L33: 0.1440 L12: 1.0092 REMARK 3 L13: -0.4441 L23: -0.3143 REMARK 3 S TENSOR REMARK 3 S11: -0.0121 S12: 0.0018 S13: 0.1329 REMARK 3 S21: -0.0248 S22: 0.0294 S23: 0.0470 REMARK 3 S31: 0.0444 S32: 0.0010 S33: -0.0173 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 1XVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030821. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97940 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18181 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.26700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1TZA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BIS-TRIS, MAGNESIUM, FORMATE, PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.06900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.99900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.06900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.99900 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS REMARK 300 UNKNOWN. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 A 406 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 LEU A 125 REMARK 465 ASN A 126 REMARK 465 LEU B 125 REMARK 465 ASN B 126 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 O HOH A 362 O HOH A 376 2.14 REMARK 500 CZ ARG B 49 O HOH B 239 2.16 REMARK 500 O HOH B 186 O HOH B 234 2.16 REMARK 500 OE2 GLU A 105 O HOH A 366 2.17 REMARK 500 OE1 GLN B 60 O HOH B 210 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 GLU A 19 CG GLU A 19 CD 0.090 REMARK 500 VAL A 93 CB VAL A 93 CG1 -0.184 REMARK 500 THR B 43 CB THR B 43 CG2 -0.320 REMARK 500 ARG B 49 CG ARG B 49 CD -0.174 REMARK 500 GLN B 106 CB GLN B 106 CG -0.185 REMARK 500 VAL B 112 CB VAL B 112 CG2 0.158 REMARK 500 ARG B 118 C ARG B 118 O 0.125 REMARK 500 ALA B 120 CA ALA B 120 CB 0.130 REMARK 500 VAL B 121 CB VAL B 121 CG2 -0.188 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 LYS A 9 CD - CE - NZ ANGL. DEV. = 14.9 DEGREES REMARK 500 ARG A 49 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 ARG A 74 NE - CZ - NH1 ANGL. DEV. = -7.6 DEGREES REMARK 500 ARG A 74 NE - CZ - NH2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 118 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 MSE B 1 CB - CG - SE ANGL. DEV. = -18.9 DEGREES REMARK 500 LEU B 46 CB - CG - CD1 ANGL. DEV. = -13.7 DEGREES REMARK 500 MSE B 47 CG - SE - CE ANGL. DEV. = 18.1 DEGREES REMARK 500 ARG B 49 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG B 49 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP B 55 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP B 66 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG B 74 NE - CZ - NH1 ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG B 74 NE - CZ - NH2 ANGL. DEV. = 6.3 DEGREES REMARK 500 GLN B 99 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 MSE B 102 CG - SE - CE ANGL. DEV. = 14.9 DEGREES REMARK 500 ARG B 118 NE - CZ - NH1 ANGL. DEV. = 4.1 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 ALA A 77 130.51 -39.68 REMARK 500 SER A 85 -154.16 -151.27 REMARK 500 HIS A 123 55.74 -152.53 REMARK 500 ASN B 22 81.87 -152.29 REMARK 500 ASN B 78 15.98 57.16 REMARK 500 VAL B 121 150.78 -43.71 REMARK 500 HIS B 123 53.13 -152.42 REMARK 500 REMARK 500 REMARK: NULL 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 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC26324 RELATED DB: TARGETDB DBREF 1XVS A 1 126 UNP Q9KUS3 APAG_VIBCH 1 126 DBREF 1XVS B 1 126 UNP Q9KUS3 APAG_VIBCH 1 126 SEQADV 1XVS MSE A 1 UNP Q9KUS3 MET 1 MODIFIED RESIDUE SEQADV 1XVS MSE A 47 UNP Q9KUS3 MET 47 MODIFIED RESIDUE SEQADV 1XVS MSE A 96 UNP Q9KUS3 MET 96 MODIFIED RESIDUE SEQADV 1XVS MSE A 102 UNP Q9KUS3 MET 102 MODIFIED RESIDUE SEQADV 1XVS MSE B 1 UNP Q9KUS3 MET 1 MODIFIED RESIDUE SEQADV 1XVS MSE B 47 UNP Q9KUS3 MET 47 MODIFIED RESIDUE SEQADV 1XVS MSE B 96 UNP Q9KUS3 MET 96 MODIFIED RESIDUE SEQADV 1XVS MSE B 102 UNP Q9KUS3 MET 102 MODIFIED RESIDUE SEQRES 1 A 126 MSE ASP VAL SER LEU PRO CYS ILE LYS ILE GLN VAL GLN SEQRES 2 A 126 THR ARG TYR ILE GLU GLU GLN SER ASN PRO GLU TYR GLN SEQRES 3 A 126 ARG PHE VAL PHE ALA TYR LEU ILE THR ILE LYS ASN LEU SEQRES 4 A 126 SER SER GLN THR VAL GLN LEU MSE SER ARG ARG TRP LEU SEQRES 5 A 126 ILE THR ASP ALA ASP GLY LYS GLN THR VAL VAL GLU GLY SEQRES 6 A 126 ASP GLY VAL VAL GLY GLU GLN PRO ARG ILE LYS ALA ASN SEQRES 7 A 126 ASP GLU TYR THR TYR SER SER GLY THR ALA LEU ASP THR SEQRES 8 A 126 PRO VAL GLY VAL MSE GLN GLY GLN TYR LEU MSE ILE ASP SEQRES 9 A 126 GLU GLN GLY GLU SER PHE THR VAL GLU ILE GLU PRO PHE SEQRES 10 A 126 ARG LEU ALA VAL PRO HIS VAL LEU ASN SEQRES 1 B 126 MSE ASP VAL SER LEU PRO CYS ILE LYS ILE GLN VAL GLN SEQRES 2 B 126 THR ARG TYR ILE GLU GLU GLN SER ASN PRO GLU TYR GLN SEQRES 3 B 126 ARG PHE VAL PHE ALA TYR LEU ILE THR ILE LYS ASN LEU SEQRES 4 B 126 SER SER GLN THR VAL GLN LEU MSE SER ARG ARG TRP LEU SEQRES 5 B 126 ILE THR ASP ALA ASP GLY LYS GLN THR VAL VAL GLU GLY SEQRES 6 B 126 ASP GLY VAL VAL GLY GLU GLN PRO ARG ILE LYS ALA ASN SEQRES 7 B 126 ASP GLU TYR THR TYR SER SER GLY THR ALA LEU ASP THR SEQRES 8 B 126 PRO VAL GLY VAL MSE GLN GLY GLN TYR LEU MSE ILE ASP SEQRES 9 B 126 GLU GLN GLY GLU SER PHE THR VAL GLU ILE GLU PRO PHE SEQRES 10 B 126 ARG LEU ALA VAL PRO HIS VAL LEU ASN MODRES 1XVS MSE A 1 MET SELENOMETHIONINE MODRES 1XVS MSE A 47 MET SELENOMETHIONINE MODRES 1XVS MSE A 96 MET SELENOMETHIONINE MODRES 1XVS MSE A 102 MET SELENOMETHIONINE MODRES 1XVS MSE B 1 MET SELENOMETHIONINE MODRES 1XVS MSE B 47 MET SELENOMETHIONINE MODRES 1XVS MSE B 96 MET SELENOMETHIONINE MODRES 1XVS MSE B 102 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 47 8 HET MSE A 96 8 HET MSE A 102 8 HET MSE B 1 8 HET MSE B 47 8 HET MSE B 96 8 HET MSE B 102 8 HET GOL A 301 6 HETNAM MSE SELENOMETHIONINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *248(H2 O) HELIX 1 1 GLU A 18 SER A 21 5 4 HELIX 2 2 ASN A 22 GLN A 26 5 5 HELIX 3 3 GLU B 18 SER B 21 5 4 HELIX 4 4 ASN B 22 GLN B 26 5 5 SHEET 1 A 3 ILE A 8 TYR A 16 0 SHEET 2 A 3 PHE A 28 ASN A 38 -1 O LEU A 33 N GLN A 13 SHEET 3 A 3 GLU A 80 LEU A 89 -1 O LEU A 89 N PHE A 28 SHEET 1 B 3 GLN A 60 ASP A 66 0 SHEET 2 B 3 VAL A 44 ASP A 55 -1 N TRP A 51 O VAL A 63 SHEET 3 B 3 ARG A 74 ILE A 75 -1 O ILE A 75 N VAL A 44 SHEET 1 C 4 GLN A 60 ASP A 66 0 SHEET 2 C 4 VAL A 44 ASP A 55 -1 N TRP A 51 O VAL A 63 SHEET 3 C 4 VAL A 93 ILE A 103 -1 O GLN A 97 N LEU A 52 SHEET 4 C 4 SER A 109 ALA A 120 -1 O PHE A 110 N MSE A 102 SHEET 1 D 3 ILE B 8 TYR B 16 0 SHEET 2 D 3 PHE B 28 ASN B 38 -1 O LEU B 33 N GLN B 13 SHEET 3 D 3 GLU B 80 LEU B 89 -1 O LEU B 89 N PHE B 28 SHEET 1 E 3 GLN B 60 ASP B 66 0 SHEET 2 E 3 VAL B 44 ASP B 55 -1 N TRP B 51 O VAL B 63 SHEET 3 E 3 ARG B 74 ILE B 75 -1 O ILE B 75 N VAL B 44 SHEET 1 F 4 GLN B 60 ASP B 66 0 SHEET 2 F 4 VAL B 44 ASP B 55 -1 N TRP B 51 O VAL B 63 SHEET 3 F 4 VAL B 93 ILE B 103 -1 O VAL B 95 N THR B 54 SHEET 4 F 4 SER B 109 ALA B 120 -1 O PHE B 110 N MSE B 102 LINK C MSE A 1 N ASP A 2 1555 1555 1.34 LINK C LEU A 46 N MSE A 47 1555 1555 1.34 LINK C MSE A 47 N SER A 48 1555 1555 1.32 LINK C VAL A 95 N MSE A 96 1555 1555 1.36 LINK C MSE A 96 N GLN A 97 1555 1555 1.35 LINK C LEU A 101 N MSE A 102 1555 1555 1.32 LINK C MSE A 102 N ILE A 103 1555 1555 1.32 LINK C MSE B 1 N ASP B 2 1555 1555 1.33 LINK C LEU B 46 N MSE B 47 1555 1555 1.36 LINK C MSE B 47 N SER B 48 1555 1555 1.30 LINK C VAL B 95 N MSE B 96 1555 1555 1.35 LINK C MSE B 96 N GLN B 97 1555 1555 1.33 LINK C LEU B 101 N MSE B 102 1555 1555 1.31 LINK C MSE B 102 N ILE B 103 1555 1555 1.33 SITE 1 AC1 10 ARG A 27 VAL A 29 ALA A 88 HOH A 305 SITE 2 AC1 10 HOH A 324 HOH A 384 ARG B 27 VAL B 29 SITE 3 AC1 10 ALA B 88 HOH B 139 CRYST1 90.138 67.998 64.002 90.00 131.43 90.00 C 1 2 1 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 0.011094 0.000000 0.009793 0.00000 SCALE2 0.000000 0.014706 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020841 0.00000 HETATM 1 N MSE A 1 8.117 -7.173 26.986 1.00 26.07 N HETATM 2 CA MSE A 1 9.218 -6.338 27.563 1.00 29.74 C HETATM 3 C MSE A 1 9.763 -5.504 26.407 1.00 26.43 C HETATM 4 O MSE A 1 9.306 -4.408 26.246 1.00 23.33 O HETATM 5 CB MSE A 1 10.253 -7.221 28.178 1.00 33.74 C HETATM 6 CG MSE A 1 11.176 -6.561 29.149 1.00 43.68 C HETATM 7 SE MSE A 1 10.393 -6.057 30.872 1.00 79.05 SE HETATM 8 CE MSE A 1 9.311 -7.824 31.695 1.00 55.65 C