HEADER TRANSFERASE 05-JAN-12 3VDN TITLE CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE, IN COMPLEX TITLE 2 WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: VLDE; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: PSEUDO-GLYCOSYLTRANSFERASE; COMPND 5 EC: 2.4.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES HYGROSCOPICUS SUBSP. LIMONEUS; SOURCE 3 ORGANISM_TAXID: 264445; SOURCE 4 GENE: VLDE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ROSSMANN FOLD, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.C.CAVALIER,Y.-S.YIM,S.ASAMIZU,D.NEAU,T.MAHMUD,Y.-H.LEE REVDAT 2 28-FEB-24 3VDN 1 REMARK REVDAT 1 09-JAN-13 3VDN 0 JRNL AUTH M.C.CAVALIER,Y.-S.YIM,S.ASAMIZU,D.NEAU,T.MAHMUD,Y.-H.LEE JRNL TITL CRYSTAL STRUCTURE OF THE VLDE, THE JRNL TITL 2 PSEUDO-GLYCOSYLTRANSFERASE, WHICH CATALYZES NON-GLYCOSIDIC JRNL TITL 3 C-N COUPLING IN VALIDAMYCIN A BIOSYNTHESIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.800 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15385 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) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 814 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) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 839 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3704 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.94000 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : -1.46000 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): 2.714 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.368 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.325 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 31.639 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.902 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.860 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3820 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5214 ; 1.556 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 472 ; 5.523 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;36.889 ;22.760 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 577 ;18.720 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 45 ;20.092 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 570 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3001 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2365 ; 0.646 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3789 ; 1.167 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1455 ; 1.881 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1425 ; 3.001 ; 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 : 3 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 : B 4 B 98 REMARK 3 ORIGIN FOR THE GROUP (A): -12.0660 -21.9530 14.0660 REMARK 3 T TENSOR REMARK 3 T11: 0.2313 T22: 0.5571 REMARK 3 T33: 0.3525 T12: -0.0371 REMARK 3 T13: 0.0750 T23: -0.1042 REMARK 3 L TENSOR REMARK 3 L11: 3.2806 L22: 1.7610 REMARK 3 L33: -0.0193 L12: -0.2839 REMARK 3 L13: -1.7464 L23: 0.2995 REMARK 3 S TENSOR REMARK 3 S11: -0.0647 S12: 0.5144 S13: -0.2168 REMARK 3 S21: 0.0090 S22: 0.0822 S23: -0.3818 REMARK 3 S31: 0.0352 S32: -0.0686 S33: -0.0175 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 99 B 268 REMARK 3 ORIGIN FOR THE GROUP (A): -32.2400 -13.7080 21.5370 REMARK 3 T TENSOR REMARK 3 T11: 0.2806 T22: 0.2738 REMARK 3 T33: 0.1980 T12: -0.0400 REMARK 3 T13: 0.0270 T23: -0.0084 REMARK 3 L TENSOR REMARK 3 L11: 1.8099 L22: 0.5240 REMARK 3 L33: 0.3369 L12: -0.2427 REMARK 3 L13: 0.3167 L23: -0.2117 REMARK 3 S TENSOR REMARK 3 S11: -0.0887 S12: 0.0519 S13: -0.1092 REMARK 3 S21: 0.0383 S22: 0.0404 S23: -0.0124 REMARK 3 S31: 0.2024 S32: -0.0227 S33: 0.0483 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 : B 269 B 481 REMARK 3 ORIGIN FOR THE GROUP (A): -19.9750 7.5790 9.1990 REMARK 3 T TENSOR REMARK 3 T11: 0.2106 T22: 0.2875 REMARK 3 T33: 0.2251 T12: -0.0472 REMARK 3 T13: 0.0113 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 0.9356 L22: 0.8692 REMARK 3 L33: 1.2558 L12: 0.2189 REMARK 3 L13: -0.1443 L23: -0.8826 REMARK 3 S TENSOR REMARK 3 S11: -0.0554 S12: 0.1225 S13: 0.1354 REMARK 3 S21: 0.0221 S22: -0.0578 S23: -0.1669 REMARK 3 S31: 0.1049 S32: 0.0398 S33: 0.1132 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3VDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069913. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16222 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 44.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.8 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL, PH 8.0, 20-35% REMARK 280 PEG3350, 3 MM GDP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 42.01450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 60.51850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.01450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 60.51850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -84.02900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 B 1 REMARK 465 THR B 2 REMARK 465 GLY B 3 REMARK 465 LEU B 264 REMARK 465 ASP B 265 REMARK 465 GLY B 266 REMARK 465 ARG B 267 REMARK 465 ALA B 482 REMARK 465 GLU B 483 REMARK 465 ARG B 484 REMARK 465 PHE B 485 REMARK 465 ASP B 486 REMARK 465 THR B 487 REMARK 465 ALA B 488 REMARK 465 PRO B 489 REMARK 465 ALA B 490 REMARK 465 VAL B 491 REMARK 465 SER B 492 REMARK 465 THR B 493 REMARK 465 ARG B 494 REMARK 465 ALA B 495 REMARK 465 ASP B 496 REMARK 465 LEU B 497 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 OD2 ASP B 233 NH1 ARG B 246 1.73 REMARK 500 O ARG B 61 CD2 LEU B 65 1.87 REMARK 500 NH1 ARG B 169 O ALA B 175 1.95 REMARK 500 OD1 ASP B 130 NH1 ARG B 133 1.96 REMARK 500 OD2 ASP B 374 NE ARG B 398 1.97 REMARK 500 CG2 THR B 71 OE1 GLU B 79 2.05 REMARK 500 O ARG B 326 ND2 ASN B 332 2.06 REMARK 500 NE1 TRP B 278 NH1 ARG B 317 2.09 REMARK 500 O SER B 146 NH2 ARG B 172 2.12 REMARK 500 NZ LYS B 295 O3B GDP B 501 2.13 REMARK 500 O ASN B 347 O GLY B 351 2.13 REMARK 500 O SER B 260 OG1 THR B 263 2.16 REMARK 500 OE1 GLU B 57 NH2 ARG B 60 2.16 REMARK 500 NE ARG B 290 O1B GDP B 501 2.16 REMARK 500 O ASP B 18 N ARG B 27 2.17 REMARK 500 OD1 ASN B 296 NH1 ARG B 299 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O TRP B 115 O HOH B 618 2455 2.18 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 CYS B 220 CB CYS B 220 SG -0.172 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 THR B 35 -71.30 70.65 REMARK 500 LEU B 74 -101.20 -122.66 REMARK 500 SER B 76 28.38 42.83 REMARK 500 LEU B 103 -82.97 -141.77 REMARK 500 ARG B 114 -52.30 78.18 REMARK 500 ASP B 158 149.73 83.03 REMARK 500 LEU B 262 42.55 -88.16 REMARK 500 ASN B 325 119.46 -161.07 REMARK 500 ASN B 379 47.47 -90.95 REMARK 500 GLN B 385 -72.46 -138.15 REMARK 500 ASN B 386 106.76 92.46 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 GDP B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VDM RELATED DB: PDB DBREF 3VDN B 1 497 UNP Q15JG1 Q15JG1_STRHY 1 497 SEQRES 1 B 497 MET THR GLY SER GLU ILE PHE LEU ALA SER LYS ARG ALA SEQRES 2 B 497 ALA ILE THR TYR ASP THR ASP PRO ALA THR GLY GLU PRO SEQRES 3 B 497 ARG ALA TRP LEU ALA PRO GLY GLY THR GLY ASN VAL VAL SEQRES 4 B 497 ALA GLU GLN ALA GLY VAL LEU ASN ILE SER TRP ILE ALA SEQRES 5 B 497 SER ALA ASP SER GLU ASP ASP ARG ARG ALA SER ALA LEU SEQRES 6 B 497 ASN PRO ASP GLY VAL THR MET GLU LEU HIS SER GLY ARG SEQRES 7 B 497 GLU ILE LEU VAL ARG LEU ILE ARG HIS ASP PRO ALA VAL SEQRES 8 B 497 PHE ARG ASN VAL GLN ASN PHE MET THR ALA ASN LEU MET SEQRES 9 B 497 TRP ALA ALA ASN ASN TYR GLY TRP ASP ARG TRP THR GLN SEQRES 10 B 497 PRO SER PHE GLY SER ASP ALA ARG GLU GLY TRP ALA ASP SEQRES 11 B 497 PHE GLY ARG PHE THR ARG ASP PHE ALA ASP ALA ILE LEU SEQRES 12 B 497 LYS SER SER ALA GLN SER ALA ASP PRO VAL TYR LEU VAL SEQRES 13 B 497 HIS ASP TYR GLN LEU VAL GLY VAL PRO ALA LEU LEU ARG SEQRES 14 B 497 GLU GLN ARG PRO ASP ALA PRO ILE LEU LEU PHE VAL HIS SEQRES 15 B 497 ILE PRO TRP PRO SER ALA ASP TYR TRP ARG ILE LEU PRO SEQRES 16 B 497 LYS GLU ILE ARG THR GLY ILE LEU HIS GLY MET LEU PRO SEQRES 17 B 497 ALA THR THR ILE GLY PHE PHE ALA ASP ARG TRP CYS ARG SEQRES 18 B 497 ASN PHE LEU GLU SER VAL ALA ASP LEU LEU PRO ASP ALA SEQRES 19 B 497 ARG ILE ASP ARG GLU ALA MET THR VAL GLU TRP ARG GLY SEQRES 20 B 497 HIS ARG THR ARG LEU ARG THR MET PRO LEU GLY TYR SER SEQRES 21 B 497 PRO LEU THR LEU ASP GLY ARG ASN PRO GLN LEU PRO GLU SEQRES 22 B 497 GLY ILE GLU GLU TRP ALA ASP GLY HIS ARG LEU VAL VAL SEQRES 23 B 497 HIS SER GLY ARG THR ASP PRO ILE LYS ASN ALA GLU ARG SEQRES 24 B 497 ALA VAL ARG ALA PHE VAL LEU ALA ALA ARG GLY GLY GLY SEQRES 25 B 497 LEU GLU LYS THR ARG MET LEU VAL ARG MET ASN PRO ASN SEQRES 26 B 497 ARG LEU TYR VAL PRO ALA ASN ALA ASP TYR VAL HIS ARG SEQRES 27 B 497 VAL GLU THR ALA VAL ALA GLU ALA ASN ALA GLU LEU GLY SEQRES 28 B 497 SER ASP THR VAL ARG ILE ASP ASN ASP ASN ASP VAL ASN SEQRES 29 B 497 HIS THR ILE ALA CYS PHE ARG ARG ALA ASP LEU LEU ILE SEQRES 30 B 497 PHE ASN SER THR VAL ASP GLY GLN ASN LEU SER THR PHE SEQRES 31 B 497 GLU ALA PRO LEU VAL ASN GLU ARG ASP ALA ASP VAL ILE SEQRES 32 B 497 LEU SER GLU THR CYS GLY ALA ALA GLU VAL LEU GLY GLU SEQRES 33 B 497 TYR CYS ARG SER VAL ASN PRO PHE ASP LEU VAL GLU GLN SEQRES 34 B 497 ALA GLU ALA ILE SER ALA ALA LEU ALA ALA GLY PRO ARG SEQRES 35 B 497 GLN ARG ALA GLU ALA ALA ALA ARG ARG ARG ASP ALA ALA SEQRES 36 B 497 ARG PRO TRP THR LEU GLU ALA TRP VAL GLN ALA GLN LEU SEQRES 37 B 497 ASP GLY LEU ALA ALA ASP HIS ALA ALA ARG THR ALA THR SEQRES 38 B 497 ALA GLU ARG PHE ASP THR ALA PRO ALA VAL SER THR ARG SEQRES 39 B 497 ALA ASP LEU HET GDP B 501 28 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 HOH *64(H2 O) HELIX 1 1 THR B 35 ALA B 40 1 6 HELIX 2 2 SER B 56 ASN B 66 1 11 HELIX 3 3 HIS B 75 GLY B 77 5 3 HELIX 4 4 ASP B 88 MET B 99 1 12 HELIX 5 5 LEU B 103 ASN B 109 1 7 HELIX 6 6 GLY B 121 SER B 146 1 26 HELIX 7 7 TYR B 159 VAL B 162 5 4 HELIX 8 8 GLY B 163 ARG B 172 1 10 HELIX 9 9 SER B 187 ARG B 192 1 6 HELIX 10 10 PRO B 195 LEU B 207 1 13 HELIX 11 11 ALA B 216 LEU B 231 1 16 HELIX 12 12 GLY B 274 ASP B 280 1 7 HELIX 13 13 ASP B 292 LYS B 295 5 4 HELIX 14 14 ASN B 296 GLY B 311 1 16 HELIX 15 15 VAL B 329 GLY B 351 1 23 HELIX 16 16 ASP B 362 ALA B 373 1 12 HELIX 17 17 LEU B 387 ALA B 392 1 6 HELIX 18 18 GLY B 409 GLY B 415 1 7 HELIX 19 19 ASP B 425 ALA B 439 1 15 HELIX 20 20 GLY B 440 ARG B 456 1 17 HELIX 21 21 THR B 459 THR B 481 1 23 SHEET 1 A10 VAL B 70 GLU B 73 0 SHEET 2 A10 GLU B 79 ILE B 85 -1 O ILE B 80 N MET B 72 SHEET 3 A10 ASN B 47 SER B 53 1 N TRP B 50 O LEU B 81 SHEET 4 A10 GLU B 5 ALA B 9 1 N ILE B 6 O ASN B 47 SHEET 5 A10 VAL B 153 HIS B 157 1 O LEU B 155 N ALA B 9 SHEET 6 A10 ILE B 177 PHE B 180 1 O LEU B 178 N VAL B 156 SHEET 7 A10 THR B 211 PHE B 214 1 O GLY B 213 N LEU B 179 SHEET 8 A10 HIS B 248 THR B 254 1 O ARG B 253 N PHE B 214 SHEET 9 A10 THR B 242 TRP B 245 -1 N TRP B 245 O HIS B 248 SHEET 10 A10 ARG B 235 ASP B 237 -1 N ARG B 235 O GLU B 244 SHEET 1 B 2 ILE B 15 THR B 19 0 SHEET 2 B 2 PRO B 26 LEU B 30 -1 O ARG B 27 N ASP B 18 SHEET 1 C 6 VAL B 355 ASN B 359 0 SHEET 2 C 6 THR B 316 ASN B 323 1 N MET B 322 O ASP B 358 SHEET 3 C 6 ARG B 283 ARG B 290 1 N VAL B 285 O LEU B 319 SHEET 4 C 6 LEU B 375 PHE B 378 1 O ILE B 377 N VAL B 286 SHEET 5 C 6 ASP B 401 SER B 405 1 O ILE B 403 N LEU B 376 SHEET 6 C 6 ARG B 419 VAL B 421 1 O ARG B 419 N VAL B 402 CISPEP 1 GLY B 33 GLY B 34 0 8.47 CISPEP 2 GLN B 117 PRO B 118 0 2.39 SITE 1 AC1 14 ARG B 290 LYS B 295 ARG B 321 ASN B 323 SITE 2 AC1 14 ASN B 361 ASP B 362 VAL B 363 THR B 366 SITE 3 AC1 14 ASP B 383 ASN B 386 LEU B 387 SER B 388 SITE 4 AC1 14 GLU B 391 HOH B 655 CRYST1 84.029 121.037 47.824 90.00 90.00 90.00 P 21 21 2 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 0.011901 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008262 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020910 0.00000