HEADER TRANSFERASE 29-JUN-07 2QGI TITLE THE UDP COMPLEX STRUCTURE OF THE SIXTH GENE PRODUCT OF THE F1-ATPASE TITLE 2 OPERON OF RHODOBACTER BLASTICUS CAVEAT 2QGI CHIRALITY ERROR AT CA CENTER OF ARG249A AND ALA206B COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP SYNTHASE SUBUNITS REGION ORF 6; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER BLASTICUS; SOURCE 3 ORGANISM_TAXID: 1075; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS KEYWDS MAJASTRIDIN, ATPASE OPERON, GLYCOSYL TRANSFERASE, ROSSMANN FOLD, UDP- KEYWDS 2 COMPLEX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.ENROTH,A.STRID REVDAT 6 30-AUG-23 2QGI 1 REMARK LINK REVDAT 5 07-MAR-18 2QGI 1 REMARK REVDAT 4 13-JUL-11 2QGI 1 VERSN REVDAT 3 24-FEB-09 2QGI 1 VERSN REVDAT 2 12-FEB-08 2QGI 1 JRNL REVDAT 1 22-JAN-08 2QGI 0 JRNL AUTH C.ENROTH,A.STRID JRNL TITL CRYSTAL STRUCTURE OF A PROTEIN, STRUCTURALLY RELATED TO JRNL TITL 2 GLYCOSYLTRANSFERASES, ENCODED IN THE RHODOBACTER BLASTICUS JRNL TITL 3 ATP OPERON. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1784 379 2008 JRNL REFN ISSN 0006-3002 JRNL PMID 18067873 JRNL DOI 10.1016/J.BBAPAP.2007.11.005 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 93484 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4687 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6404 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 361 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4040 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 721 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 18.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.06000 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): 0.070 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.352 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4178 ; 0.026 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5652 ; 2.104 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 494 ; 6.054 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 229 ;31.493 ;22.314 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 667 ;11.838 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;18.131 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 565 ; 0.274 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3317 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1971 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2834 ; 0.311 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 557 ; 0.151 ; 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): 82 ; 0.240 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 41 ; 0.218 ; 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): 2520 ; 1.514 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3922 ; 2.150 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1897 ; 3.483 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1730 ; 5.306 ; 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 2 A 249 REMARK 3 ORIGIN FOR THE GROUP (A): 86.4640 1.5870 11.1730 REMARK 3 T TENSOR REMARK 3 T11: -0.0064 T22: -0.0125 REMARK 3 T33: -0.0224 T12: -0.0046 REMARK 3 T13: -0.0120 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.1864 L22: 0.2742 REMARK 3 L33: 0.2784 L12: -0.0310 REMARK 3 L13: 0.1069 L23: 0.0114 REMARK 3 S TENSOR REMARK 3 S11: -0.0006 S12: -0.0813 S13: 0.0192 REMARK 3 S21: -0.0569 S22: -0.0246 S23: -0.0088 REMARK 3 S31: 0.0138 S32: -0.0049 S33: 0.0252 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 2 B 249 REMARK 3 ORIGIN FOR THE GROUP (A): 86.1470 -5.0830 -16.5580 REMARK 3 T TENSOR REMARK 3 T11: -0.0053 T22: -0.0157 REMARK 3 T33: -0.0227 T12: 0.0043 REMARK 3 T13: -0.0006 T23: 0.0057 REMARK 3 L TENSOR REMARK 3 L11: 0.2782 L22: 0.2697 REMARK 3 L33: 0.3260 L12: -0.0091 REMARK 3 L13: -0.1576 L23: -0.0033 REMARK 3 S TENSOR REMARK 3 S11: 0.0514 S12: 0.0682 S13: -0.0205 REMARK 3 S21: 0.0461 S22: -0.0763 S23: -0.0151 REMARK 3 S31: -0.0013 S32: -0.0171 S33: 0.0249 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 2QGI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000043569. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.043 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA CCP4_3.2.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 93646 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2NXV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM CITRATE (PH6.0) AND 75MM REMARK 280 MAGNESIUM ACETATE. MIXED 4+4UL WITH PROTEIN SAMPLE, HANGING DROP, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 298K., VAPOR DIFFUSION, HANGING REMARK 280 DROP 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 61.68500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.96400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 61.68500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.96400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE ASSYMMETRIC UNIT CONTAINS ONE BIOLOGICAL UNIT, I.E. A REMARK 300 DIMER. 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: 5340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 15230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 123.37000 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 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 426 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 958 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 985 LIES ON A SPECIAL POSITION. 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 LYS B 2 CG CD CE NZ REMARK 470 ASP B 209 CB CG OD1 OD2 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 647 O HOH B 888 2.12 REMARK 500 O HOH A 332 O HOH A 626 2.17 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 HOH A 370 O HOH B 1079 2655 1.93 REMARK 500 O HOH A 413 O HOH B 1115 1556 2.11 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 ARG A 120 CB ARG A 120 CG -0.164 REMARK 500 GLU B 83 CD GLU B 83 OE1 -0.079 REMARK 500 TYR B 203 CE1 TYR B 203 CZ 0.084 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 120 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP A 140 CB - CG - OD2 ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 225 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG B 72 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 120 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG B 225 NE - CZ - NH2 ANGL. DEV. = -4.9 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 PHE A 40 31.06 -99.41 REMARK 500 ASP A 89 -59.83 -154.67 REMARK 500 ASP A 106 88.12 -152.54 REMARK 500 PHE A 157 113.24 -160.56 REMARK 500 ASP B 89 -60.79 -153.77 REMARK 500 PHE B 157 118.47 -164.31 REMARK 500 ALA B 206 22.94 -67.01 REMARK 500 PHE B 227 57.07 -119.40 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 MN A 300 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 84 OD1 REMARK 620 2 ASP A 84 OD2 55.6 REMARK 620 3 HOH A 429 O 89.0 80.4 REMARK 620 4 HOH A 435 O 153.4 97.9 83.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 300 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 84 OD1 REMARK 620 2 ASP B 84 OD2 55.9 REMARK 620 3 UDP B 800 O1A 93.6 75.6 REMARK 620 4 UDP B 800 O1B 161.2 105.3 80.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP B 800 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NXV RELATED DB: PDB REMARK 900 THE STRUCTURE OF THE APO FORM OF THE SAME PROTEIN WITHOUT UDP DBREF 2QGI A 2 249 UNP P05449 YAT6_RHOBL 2 249 DBREF 2QGI B 2 249 UNP P05449 YAT6_RHOBL 2 249 SEQRES 1 A 248 LYS PRO VAL PRO THR TYR VAL GLN ASP LYS ASP GLU SER SEQRES 2 A 248 THR LEU MET PHE SER VAL CYS SER LEU VAL ARG ASP GLN SEQRES 3 A 248 ALA LYS TYR ASP ARG LEU LEU GLU SER PHE GLU ARG PHE SEQRES 4 A 248 GLY PHE THR PRO ASP LYS ALA GLU PHE LEU ALA ALA ASP SEQRES 5 A 248 ASN ARG GLU GLY ASN GLN PHE HIS GLY PHE SER TRP HIS SEQRES 6 A 248 LYS GLN MET LEU PRO ARG CYS LYS GLY ARG TYR VAL ILE SEQRES 7 A 248 PHE CYS HIS GLU ASP VAL GLU LEU VAL ASP ARG GLY TYR SEQRES 8 A 248 ASP ASP LEU VAL ALA ALA ILE GLU ALA LEU GLU GLU ALA SEQRES 9 A 248 ASP PRO LYS TRP LEU VAL ALA GLY VAL ALA GLY SER PRO SEQRES 10 A 248 TRP ARG PRO LEU ASN HIS SER VAL THR ALA GLN ALA LEU SEQRES 11 A 248 HIS ILE SER ASP VAL PHE GLY ASN ASP ARG ARG ARG GLY SEQRES 12 A 248 ASN VAL PRO CYS ARG VAL GLU SER LEU ASP GLU CYS PHE SEQRES 13 A 248 LEU LEU MET ARG ARG LEU LYS PRO VAL LEU ASN SER TYR SEQRES 14 A 248 ASP MET GLN GLY PHE HIS TYR TYR GLY ALA ASP LEU CYS SEQRES 15 A 248 LEU GLN ALA GLU PHE LEU GLY GLY ARG ALA TYR ALA ILE SEQRES 16 A 248 ASP PHE HIS LEU HIS HIS TYR GLY ARG ALA ILE ALA ASP SEQRES 17 A 248 GLU ASN PHE HIS ARG LEU ARG GLN GLU MET ALA GLN LYS SEQRES 18 A 248 TYR ARG ARG TRP PHE PRO GLY ARG ILE LEU HIS CYS VAL SEQRES 19 A 248 THR GLY ARG VAL ALA LEU GLY GLY GLY TRP TYR GLU ALA SEQRES 20 A 248 ARG SEQRES 1 B 248 LYS PRO VAL PRO THR TYR VAL GLN ASP LYS ASP GLU SER SEQRES 2 B 248 THR LEU MET PHE SER VAL CYS SER LEU VAL ARG ASP GLN SEQRES 3 B 248 ALA LYS TYR ASP ARG LEU LEU GLU SER PHE GLU ARG PHE SEQRES 4 B 248 GLY PHE THR PRO ASP LYS ALA GLU PHE LEU ALA ALA ASP SEQRES 5 B 248 ASN ARG GLU GLY ASN GLN PHE HIS GLY PHE SER TRP HIS SEQRES 6 B 248 LYS GLN MET LEU PRO ARG CYS LYS GLY ARG TYR VAL ILE SEQRES 7 B 248 PHE CYS HIS GLU ASP VAL GLU LEU VAL ASP ARG GLY TYR SEQRES 8 B 248 ASP ASP LEU VAL ALA ALA ILE GLU ALA LEU GLU GLU ALA SEQRES 9 B 248 ASP PRO LYS TRP LEU VAL ALA GLY VAL ALA GLY SER PRO SEQRES 10 B 248 TRP ARG PRO LEU ASN HIS SER VAL THR ALA GLN ALA LEU SEQRES 11 B 248 HIS ILE SER ASP VAL PHE GLY ASN ASP ARG ARG ARG GLY SEQRES 12 B 248 ASN VAL PRO CYS ARG VAL GLU SER LEU ASP GLU CYS PHE SEQRES 13 B 248 LEU LEU MET ARG ARG LEU LYS PRO VAL LEU ASN SER TYR SEQRES 14 B 248 ASP MET GLN GLY PHE HIS TYR TYR GLY ALA ASP LEU CYS SEQRES 15 B 248 LEU GLN ALA GLU PHE LEU GLY GLY ARG ALA TYR ALA ILE SEQRES 16 B 248 ASP PHE HIS LEU HIS HIS TYR GLY ARG ALA ILE ALA ASP SEQRES 17 B 248 GLU ASN PHE HIS ARG LEU ARG GLN GLU MET ALA GLN LYS SEQRES 18 B 248 TYR ARG ARG TRP PHE PRO GLY ARG ILE LEU HIS CYS VAL SEQRES 19 B 248 THR GLY ARG VAL ALA LEU GLY GLY GLY TRP TYR GLU ALA SEQRES 20 B 248 ARG HET MN A 300 1 HET MN B 300 1 HET UDP B 800 25 HETNAM MN MANGANESE (II) ION HETNAM UDP URIDINE-5'-DIPHOSPHATE FORMUL 3 MN 2(MN 2+) FORMUL 5 UDP C9 H14 N2 O12 P2 FORMUL 6 HOH *721(H2 O) HELIX 1 1 ASP A 26 PHE A 40 1 15 HELIX 2 2 SER A 64 LEU A 70 1 7 HELIX 3 3 PRO A 71 CYS A 73 5 3 HELIX 4 4 GLY A 91 ASP A 106 1 16 HELIX 5 5 TYR A 177 LEU A 189 1 13 HELIX 6 6 ASP A 209 ARG A 224 1 16 HELIX 7 7 GLY A 243 ALA A 248 5 6 HELIX 8 8 ASP B 26 PHE B 40 1 15 HELIX 9 9 SER B 64 LEU B 70 1 7 HELIX 10 10 PRO B 71 CYS B 73 5 3 HELIX 11 11 GLY B 91 ASP B 106 1 16 HELIX 12 12 TYR B 177 LEU B 189 1 13 HELIX 13 13 ASP B 209 ARG B 224 1 16 HELIX 14 14 GLY B 243 ALA B 248 5 6 SHEET 1 A11 THR A 6 VAL A 8 0 SHEET 2 A11 ALA B 47 ASP B 53 1 O ALA B 51 N VAL A 8 SHEET 3 A11 PHE B 18 VAL B 24 1 N VAL B 20 O GLU B 48 SHEET 4 A11 TYR B 77 HIS B 82 1 O ILE B 79 N CYS B 21 SHEET 5 A11 PHE B 157 ARG B 161 -1 O MET B 160 N VAL B 78 SHEET 6 A11 TRP B 109 GLY B 113 -1 N ALA B 112 O LEU B 159 SHEET 7 A11 ARG B 192 ALA B 195 1 O ARG B 192 N LEU B 110 SHEET 8 A11 CYS B 148 LEU B 153 -1 N VAL B 150 O ALA B 193 SHEET 9 A11 ALA B 115 PRO B 118 -1 N SER B 117 O GLU B 151 SHEET 10 A11 ALA B 130 ASP B 135 -1 O ALA B 130 N GLY B 116 SHEET 11 A11 GLY B 138 ARG B 143 -1 O ARG B 141 N ILE B 133 SHEET 1 B11 GLY A 138 ARG A 143 0 SHEET 2 B11 ALA A 130 ASP A 135 -1 N ILE A 133 O ARG A 141 SHEET 3 B11 ALA A 115 PRO A 118 -1 N GLY A 116 O ALA A 130 SHEET 4 B11 CYS A 148 LEU A 153 -1 O GLU A 151 N SER A 117 SHEET 5 B11 ARG A 192 ALA A 195 -1 O ALA A 193 N VAL A 150 SHEET 6 B11 TRP A 109 GLY A 113 1 N LEU A 110 O ARG A 192 SHEET 7 B11 PHE A 157 ARG A 161 -1 O LEU A 159 N ALA A 112 SHEET 8 B11 TYR A 77 HIS A 82 -1 N VAL A 78 O MET A 160 SHEET 9 B11 PHE A 18 VAL A 24 1 N CYS A 21 O ILE A 79 SHEET 10 B11 ALA A 47 ASP A 53 1 O GLU A 48 N VAL A 20 SHEET 11 B11 THR B 6 VAL B 8 1 O VAL B 8 N ALA A 51 SHEET 1 C 2 VAL A 85 GLU A 86 0 SHEET 2 C 2 HIS A 201 HIS A 202 -1 O HIS A 201 N GLU A 86 SHEET 1 D 2 ILE A 231 CYS A 234 0 SHEET 2 D 2 GLY A 237 ALA A 240 -1 O VAL A 239 N LEU A 232 SHEET 1 E 2 VAL B 85 GLU B 86 0 SHEET 2 E 2 HIS B 201 HIS B 202 -1 O HIS B 201 N GLU B 86 SHEET 1 F 2 ILE B 231 CYS B 234 0 SHEET 2 F 2 GLY B 237 ALA B 240 -1 O VAL B 239 N LEU B 232 LINK OD1 ASP A 84 MN MN A 300 1555 1555 2.19 LINK OD2 ASP A 84 MN MN A 300 1555 1555 2.50 LINK MN MN A 300 O HOH A 429 1555 1555 2.25 LINK MN MN A 300 O HOH A 435 1555 1555 2.24 LINK OD1 ASP B 84 MN MN B 300 1555 1555 2.16 LINK OD2 ASP B 84 MN MN B 300 1555 1555 2.47 LINK MN MN B 300 O1A UDP B 800 1555 1555 2.29 LINK MN MN B 300 O1B UDP B 800 1555 1555 2.25 CISPEP 1 VAL A 146 PRO A 147 0 2.17 CISPEP 2 VAL B 146 PRO B 147 0 4.28 SITE 1 AC1 5 HIS A 82 ASP A 84 HIS A 202 HOH A 429 SITE 2 AC1 5 HOH A 435 SITE 1 AC2 4 HIS B 82 ASP B 84 HIS B 202 UDP B 800 SITE 1 AC3 17 LEU B 23 ARG B 25 ASN B 54 ASN B 58 SITE 2 AC3 17 HIS B 82 GLU B 83 ASP B 84 PHE B 175 SITE 3 AC3 17 HIS B 202 GLY B 204 ARG B 205 MN B 300 SITE 4 AC3 17 HOH B 803 HOH B 804 HOH B 807 HOH B1119 SITE 5 AC3 17 HOH B1145 CRYST1 123.370 89.928 69.572 90.00 90.00 90.00 P 21 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 0.008106 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014374 0.00000