HEADER TRANSFERASE 25-MAR-10 3MBJ TITLE CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOMETHYLPYRIMIDINE KINASE TITLE 2 (BT_4458) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.10 A TITLE 3 RESOLUTION (RHOMBOHEDRAL FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE PHOSPHOMETHYLPYRIMIDINE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYRIDOXINE KINASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON; SOURCE 3 ORGANISM_TAXID: 226186; SOURCE 4 STRAIN: VPI-5482; SOURCE 5 GENE: BT_4458; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS PUTATIVE PHOSPHOMETHYLPYRIMIDINE KINASE, STRUCTURAL GENOMICS, JOINT KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 PSI-2, KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3MBJ 1 REMARK SEQADV LINK REVDAT 4 17-JUL-19 3MBJ 1 REMARK LINK REVDAT 3 08-NOV-17 3MBJ 1 REMARK REVDAT 2 13-JUL-11 3MBJ 1 VERSN REVDAT 1 12-MAY-10 3MBJ 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOMETHYLPYRIMIDINE JRNL TITL 2 KINASE (BT_4458) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 JRNL TITL 3 AT 2.10 A RESOLUTION (RHOMBOHEDRAL 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 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22278 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1137 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) : 1545 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2257 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 124 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 28.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.79000 REMARK 3 B22 (A**2) : -1.79000 REMARK 3 B33 (A**2) : 2.68000 REMARK 3 B12 (A**2) : -0.89000 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): 0.172 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.557 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2410 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1591 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3290 ; 1.615 ; 2.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3907 ; 0.941 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 300 ; 6.686 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 97 ;35.374 ;24.433 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 403 ;14.497 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;20.543 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 374 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2644 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 466 ; 0.001 ; 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): 1480 ; 0.759 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 590 ; 0.194 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2414 ; 1.396 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 930 ; 2.488 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 876 ; 3.698 ; 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 : 1 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 0 A 290 REMARK 3 ORIGIN FOR THE GROUP (A): -5.4084 25.2169 -14.0687 REMARK 3 T TENSOR REMARK 3 T11: 0.1340 T22: 0.1053 REMARK 3 T33: 0.1035 T12: 0.0026 REMARK 3 T13: -0.0168 T23: 0.0719 REMARK 3 L TENSOR REMARK 3 L11: 0.9364 L22: 1.2428 REMARK 3 L33: 0.2168 L12: 0.2012 REMARK 3 L13: -0.1087 L23: 0.0075 REMARK 3 S TENSOR REMARK 3 S11: -0.0417 S12: 0.1772 S13: 0.2666 REMARK 3 S21: -0.1791 S22: 0.0428 S23: 0.1118 REMARK 3 S31: -0.0522 S32: -0.0065 S33: -0.0011 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS REMARK 3 ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE REMARK 3 ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REMARK 3 REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. REMARK 3 SULFATE IONS (SO4) AND 2-METHYL-2,4-PENTANEDIOL (MPD & MRD) REMARK 3 MOLECULES FROM CRYSTALLIZATION ARE MODELED IN THE STRUCTURE. 5. REMARK 3 AN IMIDAZOLE MOLECULE (IMD) FROM THE PROTEIN BUFFER IS MODELED REMARK 3 IN THIS STRUCTURE. 6. ZINC IONS (ZN) AND A CHLORIDE ANION (CL) REMARK 3 FROM THE CRYSTALLIZATION DROP ADDITIVE ARE MODELED IN THE REMARK 3 STRUCTURE. REMARK 4 REMARK 4 3MBJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000058346. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-09 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 : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91837,0.97916,0.97871 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(111) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.5 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22278 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 29.591 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : 0.13700 REMARK 200 FOR THE DATA SET : 10.7000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.83800 REMARK 200 R SYM FOR SHELL (I) : 0.83800 REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, AUTOSHARP, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35.00% 2-METHYL-2,4-PENTANEDIOL, 0.20M REMARK 280 LITHIUM SULFATE, 0.1M MES PH 6.0, ADDITIVE: 0.001M ZINC CHLORIDE, REMARK 280 NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 80.81350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.65770 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.37933 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 80.81350 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 46.65770 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.37933 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 80.81350 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 46.65770 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 25.37933 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 80.81350 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 46.65770 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.37933 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 80.81350 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 46.65770 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 25.37933 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 80.81350 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 46.65770 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 25.37933 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 93.31539 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 50.75867 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 93.31539 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 50.75867 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 93.31539 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 50.75867 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 93.31539 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 50.75867 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 93.31539 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 50.75867 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 93.31539 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 50.75867 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: 33700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 57120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -784.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 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 ZN ZN A 291 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 ASP A 190 REMARK 465 GLU A 191 REMARK 465 PRO A 192 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 ARG A 119 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 123 CG OD1 ND2 REMARK 470 LYS A 130 CD CE NZ REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 GLU A 168 CG CD OE1 OE2 REMARK 470 HIS A 189 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 193 CG ND1 CD2 CE1 NE2 REMARK 470 MSE A 284 CG SE CE 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 20 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 279 CB - CG - OD1 ANGL. DEV. = 8.4 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 SER A 22 -132.84 52.27 REMARK 500 LEU A 114 -33.86 -136.59 REMARK 500 VAL A 188 -99.74 -106.72 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 ZN A 291 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 276 ND1 REMARK 620 2 ASP A 279 OD2 113.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 293 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 317 O REMARK 620 2 HOH A 332 O 96.6 REMARK 620 3 HOH A 337 O 92.0 131.9 REMARK 620 4 HOH A 354 O 85.5 111.7 116.1 REMARK 620 5 HOH A 398 O 169.1 92.6 86.1 85.6 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 ZN A 291 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 292 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 294 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 297 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 298 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 299 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 375199 RELATED DB: TARGETDB REMARK 900 RELATED ID: 3MBH RELATED DB: PDB REMARK 900 PUTATIVE PHOSPHOMETHYLPYRIMIDINE KINASE (BT_4458) FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON VPI-5482 AT 2.0 A RESOLUTION (ORTHORHOMBIC FORM REMARK 900 WITH PYRIDOXAL) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3MBJ A 1 290 UNP Q89ZB9 Q89ZB9_BACTN 1 290 SEQADV 3MBJ GLY A 0 UNP Q89ZB9 EXPRESSION TAG SEQRES 1 A 291 GLY MSE TYR ALA ASN LYS VAL LYS LYS ILE ALA ALA VAL SEQRES 2 A 291 HIS ASP LEU SER GLY MSE GLY ARG VAL SER LEU THR VAL SEQRES 3 A 291 VAL ILE PRO ILE LEU SER SER MSE GLY PHE GLN VAL CYS SEQRES 4 A 291 PRO LEU PRO THR ALA VAL LEU SER ASN HIS THR GLN TYR SEQRES 5 A 291 PRO GLY PHE SER PHE LEU ASP LEU THR ASP GLU MSE PRO SEQRES 6 A 291 LYS ILE ILE ALA GLU TRP LYS LYS LEU GLU VAL GLN PHE SEQRES 7 A 291 ASP ALA ILE TYR THR GLY TYR LEU GLY SER PRO ARG GLN SEQRES 8 A 291 ILE GLN ILE VAL SER ASP PHE ILE LYS ASP PHE ARG GLN SEQRES 9 A 291 PRO ASP SER LEU ILE VAL ALA ASP PRO VAL LEU GLY ASP SEQRES 10 A 291 ASN GLY ARG LEU TYR THR ASN PHE ASP MSE GLU MSE VAL SEQRES 11 A 291 LYS GLU MSE ARG HIS LEU ILE THR LYS ALA ASP VAL ILE SEQRES 12 A 291 THR PRO ASN LEU THR GLU LEU PHE TYR LEU LEU ASP GLU SEQRES 13 A 291 PRO TYR LYS ALA ASP SER THR ASP GLU GLU LEU LYS GLU SEQRES 14 A 291 TYR LEU ARG LEU LEU SER ASP LYS GLY PRO GLN VAL VAL SEQRES 15 A 291 ILE ILE THR SER VAL PRO VAL HIS ASP GLU PRO HIS LYS SEQRES 16 A 291 THR SER VAL TYR ALA TYR ASN ARG GLN GLY ASN ARG TYR SEQRES 17 A 291 TRP LYS VAL THR CYS PRO TYR LEU PRO ALA HIS TYR PRO SEQRES 18 A 291 GLY THR GLY ASP THR PHE THR SER VAL ILE THR GLY SER SEQRES 19 A 291 LEU MSE GLN GLY ASP SER LEU PRO MSE ALA LEU ASP ARG SEQRES 20 A 291 ALA THR GLN PHE ILE LEU GLN GLY ILE ARG ALA THR PHE SEQRES 21 A 291 GLY TYR GLU TYR ASP ASN ARG GLU GLY ILE LEU LEU GLU SEQRES 22 A 291 LYS VAL LEU HIS ASN LEU ASP MSE PRO ILE GLN MSE ALA SEQRES 23 A 291 SER TYR GLU LEU ILE MODRES 3MBJ MSE A 1 MET SELENOMETHIONINE MODRES 3MBJ MSE A 18 MET SELENOMETHIONINE MODRES 3MBJ MSE A 33 MET SELENOMETHIONINE MODRES 3MBJ MSE A 63 MET SELENOMETHIONINE MODRES 3MBJ MSE A 126 MET SELENOMETHIONINE MODRES 3MBJ MSE A 128 MET SELENOMETHIONINE MODRES 3MBJ MSE A 132 MET SELENOMETHIONINE MODRES 3MBJ MSE A 235 MET SELENOMETHIONINE MODRES 3MBJ MSE A 242 MET SELENOMETHIONINE MODRES 3MBJ MSE A 280 MET SELENOMETHIONINE MODRES 3MBJ MSE A 284 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 18 8 HET MSE A 33 8 HET MSE A 63 8 HET MSE A 126 8 HET MSE A 128 8 HET MSE A 132 8 HET MSE A 235 16 HET MSE A 242 16 HET MSE A 280 16 HET MSE A 284 5 HET ZN A 291 1 HET ZN A 292 1 HET ZN A 293 1 HET CL A 294 1 HET SO4 A 295 5 HET SO4 A 296 5 HET IMD A 297 5 HET MPD A 298 8 HET MRD A 299 8 HET MPD A 300 8 HET MRD A 301 8 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM IMD IMIDAZOLE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 2 ZN 3(ZN 2+) FORMUL 5 CL CL 1- FORMUL 6 SO4 2(O4 S 2-) FORMUL 8 IMD C3 H5 N2 1+ FORMUL 9 MPD 2(C6 H14 O2) FORMUL 10 MRD 2(C6 H14 O2) FORMUL 13 HOH *124(H2 O) HELIX 1 1 SER A 22 MSE A 33 1 12 HELIX 2 2 GLU A 62 GLU A 74 1 13 HELIX 3 3 SER A 87 ARG A 102 1 16 HELIX 4 4 ASP A 125 THR A 137 1 13 HELIX 5 5 ASN A 145 ASP A 154 1 10 HELIX 6 6 THR A 162 ASP A 175 1 14 HELIX 7 7 GLY A 221 GLN A 236 1 16 HELIX 8 8 SER A 239 GLY A 260 1 22 HELIX 9 9 ASP A 264 GLY A 268 5 5 HELIX 10 10 LEU A 270 LEU A 275 1 6 HELIX 11 11 HIS A 276 MSE A 280 5 5 SHEET 1 A 9 GLN A 36 PRO A 39 0 SHEET 2 A 9 LYS A 8 VAL A 12 1 N ILE A 9 O GLN A 36 SHEET 3 A 9 ALA A 79 THR A 82 1 O TYR A 81 N ALA A 10 SHEET 4 A 9 LEU A 107 ALA A 110 1 O VAL A 109 N ILE A 80 SHEET 5 A 9 VAL A 141 ILE A 142 1 O VAL A 141 N ALA A 110 SHEET 6 A 9 VAL A 180 PRO A 187 1 O ILE A 182 N ILE A 142 SHEET 7 A 9 LYS A 194 ASN A 201 -1 O SER A 196 N VAL A 186 SHEET 8 A 9 ARG A 206 PRO A 213 -1 O CYS A 212 N THR A 195 SHEET 9 A 9 GLU A 288 ILE A 290 -1 O ILE A 290 N TYR A 207 SHEET 1 B 3 LEU A 15 MSE A 18 0 SHEET 2 B 3 ALA A 43 ASN A 47 1 O LEU A 45 N LEU A 15 SHEET 3 B 3 PHE A 56 ASP A 58 -1 O LEU A 57 N VAL A 44 SHEET 1 C 2 GLY A 115 ASP A 116 0 SHEET 2 C 2 ARG A 119 LEU A 120 -1 O ARG A 119 N ASP A 116 LINK C GLY A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N TYR A 2 1555 1555 1.34 LINK C GLY A 17 N MSE A 18 1555 1555 1.33 LINK C MSE A 18 N GLY A 19 1555 1555 1.32 LINK C SER A 32 N MSE A 33 1555 1555 1.35 LINK C MSE A 33 N GLY A 34 1555 1555 1.34 LINK C GLU A 62 N MSE A 63 1555 1555 1.33 LINK C MSE A 63 N PRO A 64 1555 1555 1.36 LINK C ASP A 125 N MSE A 126 1555 1555 1.33 LINK C MSE A 126 N GLU A 127 1555 1555 1.33 LINK C GLU A 127 N MSE A 128 1555 1555 1.32 LINK C MSE A 128 N VAL A 129 1555 1555 1.34 LINK C GLU A 131 N MSE A 132 1555 1555 1.34 LINK C MSE A 132 N ARG A 133 1555 1555 1.33 LINK C LEU A 234 N AMSE A 235 1555 1555 1.33 LINK C LEU A 234 N BMSE A 235 1555 1555 1.32 LINK C AMSE A 235 N GLN A 236 1555 1555 1.34 LINK C BMSE A 235 N GLN A 236 1555 1555 1.33 LINK C PRO A 241 N AMSE A 242 1555 1555 1.34 LINK C PRO A 241 N BMSE A 242 1555 1555 1.33 LINK C AMSE A 242 N ALA A 243 1555 1555 1.33 LINK C BMSE A 242 N ALA A 243 1555 1555 1.33 LINK C ASP A 279 N AMSE A 280 1555 1555 1.35 LINK C ASP A 279 N BMSE A 280 1555 1555 1.34 LINK C AMSE A 280 N PRO A 281 1555 1555 1.34 LINK C BMSE A 280 N PRO A 281 1555 1555 1.34 LINK C GLN A 283 N MSE A 284 1555 1555 1.33 LINK C MSE A 284 N ALA A 285 1555 1555 1.33 LINK OD2 ASP A 96 ZN ZN A 292 1555 1555 2.20 LINK ND1 HIS A 276 ZN ZN A 291 1555 1555 2.07 LINK OD2 ASP A 279 ZN ZN A 291 1555 1555 2.05 LINK ZN ZN A 293 O HOH A 317 1555 1555 2.29 LINK ZN ZN A 293 O HOH A 332 1555 1555 2.37 LINK ZN ZN A 293 O HOH A 337 1555 1555 2.42 LINK ZN ZN A 293 O HOH A 354 1555 1555 2.09 LINK ZN ZN A 293 O HOH A 398 1555 1555 2.05 SITE 1 AC1 2 HIS A 276 ASP A 279 SITE 1 AC2 4 ASP A 96 GLU A 131 HIS A 134 IMD A 297 SITE 1 AC3 5 HOH A 317 HOH A 332 HOH A 337 HOH A 354 SITE 2 AC3 5 HOH A 398 SITE 1 AC4 1 ALA A 3 SITE 1 AC5 10 HIS A 218 TYR A 219 PRO A 220 GLY A 221 SITE 2 AC5 10 THR A 222 GLY A 223 HOH A 328 HOH A 396 SITE 3 AC5 10 HOH A 398 HOH A 411 SITE 1 AC6 4 ILE A 98 LYS A 99 ARG A 102 LYS A 138 SITE 1 AC7 6 GLN A 92 SER A 95 ASP A 96 GLU A 131 SITE 2 AC7 6 HIS A 134 ZN A 292 SITE 1 AC8 4 GLU A 74 VAL A 75 PHE A 101 GLN A 103 SITE 1 AC9 2 GLN A 179 LEU A 240 SITE 1 BC1 5 ARG A 206 TRP A 208 PHE A 259 TYR A 261 SITE 2 BC1 5 GLU A 262 SITE 1 BC2 5 PRO A 216 PHE A 259 TYR A 287 GLU A 288 SITE 2 BC2 5 LEU A 289 CRYST1 161.627 161.627 76.138 90.00 90.00 120.00 H 3 2 18 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 0.006187 0.003572 0.000000 0.00000 SCALE2 0.000000 0.007144 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013134 0.00000