HEADER TRANSFERASE 10-MAY-12 4F4A TITLE CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE B FROM TRYPANOSOMA TITLE 2 BRUCEI, UDP-BOUND FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: NUCLEOSIDE DIPHOSPHATE KINASE B; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI BRUCEI; SOURCE 3 ORGANISM_TAXID: 999953; SOURCE 4 STRAIN: 927/4 GUTAT10.1; SOURCE 5 GENE: TB11.01.7800; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: AVA0421 KEYWDS SSGCID, NIH, NIAID, SBRI, EMERALD BIOSTRUCTURES, STRUCTURAL GENOMICS, KEYWDS 2 SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 2 28-FEB-24 4F4A 1 REMARK SEQADV LINK REVDAT 1 30-MAY-12 4F4A 0 JRNL AUTH SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE JRNL AUTH 2 (SSGCID),A.S.GARDBERG,T.E.EDWARDS,B.STAKER,L.STEWART JRNL TITL CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE B FROM JRNL TITL 2 TRYPANOSOMA BRUCEI, UDP-BOUND FORM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 28728 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) : 0.158 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1444 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1784 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.1670 REMARK 3 BIN FREE R VALUE SET COUNT : 101 REMARK 3 BIN FREE R VALUE : 0.2300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3499 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 416 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.15000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.27000 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): 0.202 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.428 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3666 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2504 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4976 ; 1.460 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6096 ; 1.146 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 453 ; 5.808 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 153 ;31.264 ;23.725 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 602 ;11.972 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;26.271 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 541 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4031 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 762 ; 0.005 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 151 REMARK 3 RESIDUE RANGE : A 201 A 202 REMARK 3 ORIGIN FOR THE GROUP (A): 17.3711 14.0303 37.4601 REMARK 3 T TENSOR REMARK 3 T11: 0.0116 T22: 0.0518 REMARK 3 T33: 0.0235 T12: 0.0181 REMARK 3 T13: 0.0012 T23: 0.0092 REMARK 3 L TENSOR REMARK 3 L11: 0.6235 L22: 1.0742 REMARK 3 L33: 0.4986 L12: -0.0804 REMARK 3 L13: -0.0412 L23: -0.1296 REMARK 3 S TENSOR REMARK 3 S11: -0.0590 S12: -0.1008 S13: -0.0517 REMARK 3 S21: 0.0729 S22: 0.0381 S23: -0.0584 REMARK 3 S31: 0.0112 S32: 0.0902 S33: 0.0209 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 151 REMARK 3 RESIDUE RANGE : B 201 B 202 REMARK 3 ORIGIN FOR THE GROUP (A): 15.4394 17.4776 13.6591 REMARK 3 T TENSOR REMARK 3 T11: 0.0290 T22: 0.0753 REMARK 3 T33: 0.0295 T12: 0.0002 REMARK 3 T13: 0.0236 T23: -0.0139 REMARK 3 L TENSOR REMARK 3 L11: 1.1654 L22: 0.4613 REMARK 3 L33: 0.6527 L12: 0.1881 REMARK 3 L13: -0.0104 L23: -0.1522 REMARK 3 S TENSOR REMARK 3 S11: -0.0134 S12: 0.1689 S13: -0.0364 REMARK 3 S21: -0.0728 S22: -0.0030 S23: -0.0333 REMARK 3 S31: 0.0069 S32: 0.1191 S33: 0.0164 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 152 REMARK 3 RESIDUE RANGE : C 201 C 202 REMARK 3 ORIGIN FOR THE GROUP (A): 3.6053 44.3974 39.9069 REMARK 3 T TENSOR REMARK 3 T11: 0.0858 T22: 0.0072 REMARK 3 T33: 0.0165 T12: -0.0089 REMARK 3 T13: -0.0041 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 0.7841 L22: 0.6715 REMARK 3 L33: 0.3702 L12: 0.2742 REMARK 3 L13: 0.1260 L23: 0.1397 REMARK 3 S TENSOR REMARK 3 S11: -0.0081 S12: -0.0412 S13: 0.0344 REMARK 3 S21: 0.0624 S22: 0.0072 S23: -0.0175 REMARK 3 S31: -0.1344 S32: 0.0130 S33: 0.0009 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: U VALUES : WITH TLS ADDED REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 4F4A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072436. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541780 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28728 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 41.744 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.25700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: EBS INTERNAL TRACKING NUMBER 234285A5: REMARK 280 JCSG A5, PROTEIN: 20.2 MG/ML TRBRA.00438.A.B1 PS01459 IN 25 MM REMARK 280 HEPES, PH 7.0, 500 MM SODIUM CHLORIDE, 2 MM DTT, 0.025% SODIUM REMARK 280 AZIDE, 5% GLYCEROL, CRYSTALLANT: 20% PEG3350, 200 MM MAGNESIUM REMARK 280 FORMATE, 2 MM UDP, 10 MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 56.58500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.58500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 35.91500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.75500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.91500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.75500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.58500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.91500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 60.75500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.58500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.91500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 60.75500 REMARK 290 SMTRY3 8 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 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -164.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 56.58500 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 394 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 GLY A -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ARG A 152 REMARK 465 ALA A 153 REMARK 465 GLY B -3 REMARK 465 PRO B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ARG B 152 REMARK 465 ALA B 153 REMARK 465 GLY C -3 REMARK 465 PRO C -2 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 ALA C 153 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 A 57 CG CD CE NZ REMARK 470 LYS A 147 CG CD CE NZ REMARK 470 LYS C 134 CG CD CE NZ REMARK 470 ARG C 152 CG CD NE CZ NH1 NH2 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 OH TYR A 66 O HOH B 370 3555 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 HIS B 50 CG HIS B 50 CD2 0.056 REMARK 500 HIS B 144 CG HIS B 144 CD2 0.057 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 VAL A 115 -34.48 78.11 REMARK 500 VAL B 115 -34.34 76.37 REMARK 500 VAL C 115 -32.87 79.02 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 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UDP A 201 O2A REMARK 620 2 UDP A 201 O3B 71.5 REMARK 620 3 HOH A 384 O 76.1 73.6 REMARK 620 4 HOH A 385 O 145.7 80.0 78.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UDP B 201 O3B REMARK 620 2 UDP B 201 O2A 80.4 REMARK 620 3 HOH B 356 O 99.7 86.8 REMARK 620 4 HOH B 406 O 97.4 174.0 99.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UDP C 201 O3B REMARK 620 2 UDP C 201 O2A 86.9 REMARK 620 3 HOH C 381 O 88.7 173.5 REMARK 620 4 HOH C 382 O 90.5 87.4 87.9 REMARK 620 5 HOH C 383 O 121.9 86.8 99.7 146.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F36 RELATED DB: PDB REMARK 900 APO FORM REMARK 900 RELATED ID: SSGCID-TRBRA.00438.A RELATED DB: TARGETTRACK DBREF 4F4A A 1 153 UNP Q381H3 Q381H3_TRYB2 1 153 DBREF 4F4A B 1 153 UNP Q381H3 Q381H3_TRYB2 1 153 DBREF 4F4A C 1 153 UNP Q381H3 Q381H3_TRYB2 1 153 SEQADV 4F4A GLY A -3 UNP Q381H3 EXPRESSION TAG SEQADV 4F4A PRO A -2 UNP Q381H3 EXPRESSION TAG SEQADV 4F4A GLY A -1 UNP Q381H3 EXPRESSION TAG SEQADV 4F4A SER A 0 UNP Q381H3 EXPRESSION TAG SEQADV 4F4A GLY B -3 UNP Q381H3 EXPRESSION TAG SEQADV 4F4A PRO B -2 UNP Q381H3 EXPRESSION TAG SEQADV 4F4A GLY B -1 UNP Q381H3 EXPRESSION TAG SEQADV 4F4A SER B 0 UNP Q381H3 EXPRESSION TAG SEQADV 4F4A GLY C -3 UNP Q381H3 EXPRESSION TAG SEQADV 4F4A PRO C -2 UNP Q381H3 EXPRESSION TAG SEQADV 4F4A GLY C -1 UNP Q381H3 EXPRESSION TAG SEQADV 4F4A SER C 0 UNP Q381H3 EXPRESSION TAG SEQRES 1 A 157 GLY PRO GLY SER MET PRO SER GLU ARG THR PHE ILE ALA SEQRES 2 A 157 VAL LYS PRO ASP GLY VAL GLN ARG ASN LEU VAL GLY GLU SEQRES 3 A 157 ILE ILE LYS ARG PHE GLU ASN LYS GLY TYR LYS LEU VAL SEQRES 4 A 157 GLY LEU LYS LEU LEU GLN PRO THR GLU GLU GLN ALA LYS SEQRES 5 A 157 GLN HIS TYR ILE ASP LEU ALA SER LYS PRO PHE TYR SER SEQRES 6 A 157 GLY LEU VAL SER TYR PHE SER SER GLY PRO ILE VAL GLY SEQRES 7 A 157 MET VAL TRP GLU GLY LEU GLY VAL VAL LYS GLY GLY ARG SEQRES 8 A 157 VAL LEU LEU GLY ALA THR ASN PRO ALA ASP SER LEU PRO SEQRES 9 A 157 GLY THR ILE ARG GLY ASP PHE ALA VAL ASP VAL GLY ARG SEQRES 10 A 157 ASN VAL CYS HIS GLY SER ASP SER VAL GLU SER ALA LYS SEQRES 11 A 157 ARG GLU ILE ALA PHE TRP PHE LYS ALA GLU GLU LEU VAL SEQRES 12 A 157 SER TRP THR SER HIS SER VAL LYS GLN ILE TYR GLU ARG SEQRES 13 A 157 ALA SEQRES 1 B 157 GLY PRO GLY SER MET PRO SER GLU ARG THR PHE ILE ALA SEQRES 2 B 157 VAL LYS PRO ASP GLY VAL GLN ARG ASN LEU VAL GLY GLU SEQRES 3 B 157 ILE ILE LYS ARG PHE GLU ASN LYS GLY TYR LYS LEU VAL SEQRES 4 B 157 GLY LEU LYS LEU LEU GLN PRO THR GLU GLU GLN ALA LYS SEQRES 5 B 157 GLN HIS TYR ILE ASP LEU ALA SER LYS PRO PHE TYR SER SEQRES 6 B 157 GLY LEU VAL SER TYR PHE SER SER GLY PRO ILE VAL GLY SEQRES 7 B 157 MET VAL TRP GLU GLY LEU GLY VAL VAL LYS GLY GLY ARG SEQRES 8 B 157 VAL LEU LEU GLY ALA THR ASN PRO ALA ASP SER LEU PRO SEQRES 9 B 157 GLY THR ILE ARG GLY ASP PHE ALA VAL ASP VAL GLY ARG SEQRES 10 B 157 ASN VAL CYS HIS GLY SER ASP SER VAL GLU SER ALA LYS SEQRES 11 B 157 ARG GLU ILE ALA PHE TRP PHE LYS ALA GLU GLU LEU VAL SEQRES 12 B 157 SER TRP THR SER HIS SER VAL LYS GLN ILE TYR GLU ARG SEQRES 13 B 157 ALA SEQRES 1 C 157 GLY PRO GLY SER MET PRO SER GLU ARG THR PHE ILE ALA SEQRES 2 C 157 VAL LYS PRO ASP GLY VAL GLN ARG ASN LEU VAL GLY GLU SEQRES 3 C 157 ILE ILE LYS ARG PHE GLU ASN LYS GLY TYR LYS LEU VAL SEQRES 4 C 157 GLY LEU LYS LEU LEU GLN PRO THR GLU GLU GLN ALA LYS SEQRES 5 C 157 GLN HIS TYR ILE ASP LEU ALA SER LYS PRO PHE TYR SER SEQRES 6 C 157 GLY LEU VAL SER TYR PHE SER SER GLY PRO ILE VAL GLY SEQRES 7 C 157 MET VAL TRP GLU GLY LEU GLY VAL VAL LYS GLY GLY ARG SEQRES 8 C 157 VAL LEU LEU GLY ALA THR ASN PRO ALA ASP SER LEU PRO SEQRES 9 C 157 GLY THR ILE ARG GLY ASP PHE ALA VAL ASP VAL GLY ARG SEQRES 10 C 157 ASN VAL CYS HIS GLY SER ASP SER VAL GLU SER ALA LYS SEQRES 11 C 157 ARG GLU ILE ALA PHE TRP PHE LYS ALA GLU GLU LEU VAL SEQRES 12 C 157 SER TRP THR SER HIS SER VAL LYS GLN ILE TYR GLU ARG SEQRES 13 C 157 ALA HET UDP A 201 25 HET MG A 202 1 HET UDP B 201 25 HET MG B 202 1 HET UDP C 201 25 HET MG C 202 1 HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 4 UDP 3(C9 H14 N2 O12 P2) FORMUL 5 MG 3(MG 2+) FORMUL 10 HOH *416(H2 O) HELIX 1 1 LYS A 11 ARG A 17 1 7 HELIX 2 2 LEU A 19 GLY A 31 1 13 HELIX 3 3 THR A 43 TYR A 51 1 9 HELIX 4 4 ILE A 52 ALA A 55 5 4 HELIX 5 5 PHE A 59 SER A 68 1 10 HELIX 6 6 GLY A 81 GLY A 91 1 11 HELIX 7 7 ASN A 94 SER A 98 5 5 HELIX 8 8 THR A 102 ALA A 108 1 7 HELIX 9 9 ASP A 110 ASN A 114 5 5 HELIX 10 10 SER A 121 PHE A 133 1 13 HELIX 11 11 LYS A 134 LEU A 138 5 5 HELIX 12 12 SER A 145 TYR A 150 1 6 HELIX 13 13 LYS B 11 ARG B 17 1 7 HELIX 14 14 LEU B 19 GLY B 31 1 13 HELIX 15 15 THR B 43 TYR B 51 1 9 HELIX 16 16 ILE B 52 ALA B 55 5 4 HELIX 17 17 PHE B 59 SER B 68 1 10 HELIX 18 18 GLY B 81 GLY B 91 1 11 HELIX 19 19 ASN B 94 SER B 98 5 5 HELIX 20 20 THR B 102 ALA B 108 1 7 HELIX 21 21 ASP B 110 ASN B 114 5 5 HELIX 22 22 SER B 121 PHE B 133 1 13 HELIX 23 23 LYS B 134 LEU B 138 5 5 HELIX 24 24 SER B 145 TYR B 150 1 6 HELIX 25 25 LYS C 11 ARG C 17 1 7 HELIX 26 26 LEU C 19 GLY C 31 1 13 HELIX 27 27 THR C 43 TYR C 51 1 9 HELIX 28 28 ILE C 52 ALA C 55 5 4 HELIX 29 29 PHE C 59 SER C 68 1 10 HELIX 30 30 GLY C 81 GLY C 91 1 11 HELIX 31 31 ASN C 94 SER C 98 5 5 HELIX 32 32 THR C 102 ALA C 108 1 7 HELIX 33 33 ASP C 110 ASN C 114 5 5 HELIX 34 34 SER C 121 PHE C 133 1 13 HELIX 35 35 LYS C 134 LEU C 138 5 5 HELIX 36 36 SER C 145 TYR C 150 1 6 SHEET 1 A 4 LYS A 33 LEU A 40 0 SHEET 2 A 4 ILE A 72 GLU A 78 -1 O ILE A 72 N LEU A 40 SHEET 3 A 4 ARG A 5 VAL A 10 -1 N ILE A 8 O MET A 75 SHEET 4 A 4 CYS A 116 GLY A 118 -1 O HIS A 117 N ALA A 9 SHEET 1 B 4 LYS B 33 LEU B 40 0 SHEET 2 B 4 ILE B 72 GLU B 78 -1 O GLY B 74 N LYS B 38 SHEET 3 B 4 ARG B 5 VAL B 10 -1 N ILE B 8 O MET B 75 SHEET 4 B 4 CYS B 116 GLY B 118 -1 O HIS B 117 N ALA B 9 SHEET 1 C 4 LYS C 33 LEU C 40 0 SHEET 2 C 4 ILE C 72 GLU C 78 -1 O ILE C 72 N LEU C 40 SHEET 3 C 4 ARG C 5 VAL C 10 -1 N ILE C 8 O MET C 75 SHEET 4 C 4 CYS C 116 GLY C 118 -1 O HIS C 117 N ALA C 9 LINK O2A UDP A 201 MG MG A 202 1555 1555 2.19 LINK O3B UDP A 201 MG MG A 202 1555 1555 2.20 LINK MG MG A 202 O HOH A 384 1555 1555 2.55 LINK MG MG A 202 O HOH A 385 1555 1555 2.25 LINK O3B UDP B 201 MG MG B 202 1555 1555 1.93 LINK O2A UDP B 201 MG MG B 202 1555 1555 2.25 LINK MG MG B 202 O HOH B 356 1555 1555 2.06 LINK MG MG B 202 O HOH B 406 1555 1555 2.15 LINK O3B UDP C 201 MG MG C 202 1555 1555 1.96 LINK O2A UDP C 201 MG MG C 202 1555 1555 2.11 LINK MG MG C 202 O HOH C 381 1555 1555 2.20 LINK MG MG C 202 O HOH C 382 1555 1555 2.01 LINK MG MG C 202 O HOH C 383 1555 1555 2.03 SITE 1 AC1 16 LYS A 11 TYR A 51 LEU A 54 PHE A 59 SITE 2 AC1 16 LEU A 63 ARG A 87 THR A 93 VAL A 111 SITE 3 AC1 16 ASN A 114 MG A 202 HOH A 311 HOH A 316 SITE 4 AC1 16 HOH A 330 HOH A 384 HOH A 385 HOH A 407 SITE 1 AC2 3 UDP A 201 HOH A 384 HOH A 385 SITE 1 AC3 16 LYS B 11 LEU B 54 PHE B 59 LEU B 63 SITE 2 AC3 16 ARG B 87 THR B 93 VAL B 111 GLY B 112 SITE 3 AC3 16 ASN B 114 MG B 202 HOH B 302 HOH B 356 SITE 4 AC3 16 HOH B 365 HOH B 395 HOH B 406 HOH C 420 SITE 1 AC4 3 UDP B 201 HOH B 356 HOH B 406 SITE 1 AC5 19 LYS C 11 TYR C 51 LEU C 54 PHE C 59 SITE 2 AC5 19 LEU C 63 ARG C 87 THR C 93 VAL C 111 SITE 3 AC5 19 ASN C 114 MG C 202 HOH C 312 HOH C 321 SITE 4 AC5 19 HOH C 381 HOH C 382 HOH C 383 HOH C 386 SITE 5 AC5 19 HOH C 387 HOH C 408 HOH C 435 SITE 1 AC6 4 UDP C 201 HOH C 381 HOH C 382 HOH C 383 CRYST1 71.830 121.510 113.170 90.00 90.00 90.00 C 2 2 21 24 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 0.013922 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008230 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008836 0.00000