HEADER TRANSFERASE 24-FEB-11 3QUR TITLE CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM TITLE 2 STREPTOMYCES WEDMORENSIS COMPLEXED WITH MGADP AND FOSFOMYCIN TITLE 3 MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FOMA PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES WEDMORENSIS; SOURCE 3 ORGANISM_TAXID: 43759; SOURCE 4 GENE: FOMA, FOSFOMYCIN RESISTANCE KINASE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS FOSFOMYCIN, ANTIBIOTIC RESISTANCE, PHOSPHORYL TRANSFER, KINASE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.PAKHOMOVA,S.G.BARTLETT,P.A.DOERNER,M.E.NEWCOMER REVDAT 4 13-SEP-23 3QUR 1 REMARK SEQADV LINK REVDAT 3 29-FEB-12 3QUR 1 JRNL REVDAT 2 27-JUL-11 3QUR 1 HEADER REVDAT 1 20-JUL-11 3QUR 0 JRNL AUTH S.PAKHOMOVA,S.G.BARTLETT,P.A.DOERNER,M.E.NEWCOMER JRNL TITL STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO THE MECHANISM OF JRNL TITL 2 FOSFOMYCIN PHOSPHORYLATION BY FOSFOMYCIN RESISTANCE KINASE JRNL TITL 3 FOMA. JRNL REF BIOCHEMISTRY V. 50 6909 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21728358 JRNL DOI 10.1021/BI2004334 REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 43681 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.500 REMARK 3 FREE R VALUE TEST SET COUNT : 684 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) : 1.57 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.61 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2322 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.4090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1889 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 232 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : 0.58000 REMARK 3 B33 (A**2) : -0.87000 REMARK 3 B12 (A**2) : 0.29000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.063 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.677 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2010 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1370 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2736 ; 2.154 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3309 ; 1.122 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 249 ; 6.106 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;31.693 ;21.807 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 320 ;14.104 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;20.779 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 314 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2206 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 431 ; 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): 1250 ; 1.349 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 511 ; 0.379 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2004 ; 2.332 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 760 ; 3.244 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 729 ; 5.160 ; 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 -8 A 55 REMARK 3 ORIGIN FOR THE GROUP (A): 26.0284 16.9992 14.0534 REMARK 3 T TENSOR REMARK 3 T11: 0.0363 T22: 0.0588 REMARK 3 T33: 0.0273 T12: 0.0284 REMARK 3 T13: 0.0096 T23: 0.0374 REMARK 3 L TENSOR REMARK 3 L11: 2.3776 L22: 2.3682 REMARK 3 L33: 1.7343 L12: 0.7795 REMARK 3 L13: 0.6329 L23: 0.7692 REMARK 3 S TENSOR REMARK 3 S11: -0.0484 S12: -0.2894 S13: -0.2323 REMARK 3 S21: 0.0140 S22: 0.0629 S23: 0.0182 REMARK 3 S31: 0.2175 S32: 0.0942 S33: -0.0145 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 : A 69 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): 30.9773 19.6556 6.3037 REMARK 3 T TENSOR REMARK 3 T11: 0.0370 T22: 0.0247 REMARK 3 T33: 0.0458 T12: 0.0062 REMARK 3 T13: 0.0104 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 1.1709 L22: 0.5604 REMARK 3 L33: 0.9616 L12: -0.3067 REMARK 3 L13: 0.1646 L23: -0.0916 REMARK 3 S TENSOR REMARK 3 S11: 0.0104 S12: -0.0266 S13: -0.0427 REMARK 3 S21: 0.0106 S22: -0.0085 S23: -0.0271 REMARK 3 S31: 0.0988 S32: 0.1205 S33: -0.0019 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 3QUR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000064128. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CAMD REMARK 200 BEAMLINE : GCPCC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.38079 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47552 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 25.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45900 REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 3D40 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: 17 % PEG3350, 25 % GLYCEROL, 0.1 M REMARK 280 MES, 10 MM ADP, 50 MM MGCL2, 10MM FOSFOMYCIN MONOPHOSPHATE , PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 52.82000 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 26.41000 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 26.41000 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 52.82000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 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 A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 PHE A 56 REMARK 465 GLY A 57 REMARK 465 HIS A 58 REMARK 465 GLY A 59 REMARK 465 ALA A 60 REMARK 465 ILE A 61 REMARK 465 ARG A 62 REMARK 465 ASP A 63 REMARK 465 HIS A 64 REMARK 465 ASP A 65 REMARK 465 SER A 66 REMARK 465 THR A 67 REMARK 465 HIS A 68 REMARK 465 GLY A 179 REMARK 465 ALA A 180 REMARK 465 GLY A 181 REMARK 465 GLY A 182 REMARK 465 GLU A 206 REMARK 465 TRP A 207 REMARK 465 ASP A 208 REMARK 465 ALA A 209 REMARK 465 THR A 210 REMARK 465 THR A 263 REMARK 465 ALA A 264 REMARK 465 SER A 265 REMARK 465 ALA A 266 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 SER A -8 OG REMARK 470 LYS A 18 CG CD CE NZ REMARK 470 SER A 205 OG 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 VAL A 160 O HOH A 308 1.72 REMARK 500 O HOH A 272 O HOH A 370 1.94 REMARK 500 OG SER A 193 O HOH A 338 2.04 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 413 O HOH A 413 4555 2.19 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 MET A 1 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 91 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 96 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 96 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 121 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 MET A 159 CA - CB - CG ANGL. DEV. = 12.3 DEGREES REMARK 500 MET A 159 CG - SD - CE ANGL. DEV. = -12.6 DEGREES REMARK 500 LEU A 186 CA - CB - CG ANGL. DEV. = 16.2 DEGREES REMARK 500 ARG A 226 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 259 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 259 NE - CZ - NH2 ANGL. DEV. = -5.0 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 15 15.89 -144.64 REMARK 500 TYR A 43 40.94 -96.89 REMARK 500 TYR A 43 48.46 -86.53 REMARK 500 SER A 193 76.95 -162.10 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 A3000 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 435 O REMARK 620 2 ADP A1260 O2A 170.8 REMARK 620 3 ADP A1260 O1B 105.3 75.0 REMARK 620 4 FM4 A2000 O2 83.0 105.6 70.7 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 ADP A 1260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FM4 A 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 3000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3D41 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM REMARK 900 STREPTOMYCES WEDMORENSIS COMPLEXED WITH MGAMPPNP AND FOSFOMYCIN REMARK 900 RELATED ID: 3D40 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM REMARK 900 STREPTOMYCES WEDMORENSIS COMPLEXED WITH DIPHOSPHATE REMARK 900 RELATED ID: 3QUO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM REMARK 900 STREPTOMYCES WEDMORENSIS COMPLEXED WITH ATP AND FOSFOMYCIN REMARK 900 RELATED ID: 3QUN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM REMARK 900 STREPTOMYCES WEDMORENSIS COMPLEXED WITH MGATP REMARK 900 RELATED ID: 3QVF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM REMARK 900 STREPTOMYCES WEDMORENSIS COMPLEXED WITH MGADPAND FOSFOMYCIN VANADATE REMARK 900 RELATED ID: 3QVH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM REMARK 900 RESTREPTOMYCES WEDMORENSIS COMPLEXED WITH ADP REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHORS STATE THAT THE DEPOSITED SEQUENCE UNPROT ENTRY Q56187 REMARK 999 IS WRONG AT POSITION 31 DBREF 3QUR A 1 266 UNP Q56187 Q56187_STRWE 1 266 SEQADV 3QUR MET A -19 UNP Q56187 EXPRESSION TAG SEQADV 3QUR GLY A -18 UNP Q56187 EXPRESSION TAG SEQADV 3QUR SER A -17 UNP Q56187 EXPRESSION TAG SEQADV 3QUR SER A -16 UNP Q56187 EXPRESSION TAG SEQADV 3QUR HIS A -15 UNP Q56187 EXPRESSION TAG SEQADV 3QUR HIS A -14 UNP Q56187 EXPRESSION TAG SEQADV 3QUR HIS A -13 UNP Q56187 EXPRESSION TAG SEQADV 3QUR HIS A -12 UNP Q56187 EXPRESSION TAG SEQADV 3QUR HIS A -11 UNP Q56187 EXPRESSION TAG SEQADV 3QUR HIS A -10 UNP Q56187 EXPRESSION TAG SEQADV 3QUR SER A -9 UNP Q56187 EXPRESSION TAG SEQADV 3QUR SER A -8 UNP Q56187 EXPRESSION TAG SEQADV 3QUR GLY A -7 UNP Q56187 EXPRESSION TAG SEQADV 3QUR LEU A -6 UNP Q56187 EXPRESSION TAG SEQADV 3QUR VAL A -5 UNP Q56187 EXPRESSION TAG SEQADV 3QUR PRO A -4 UNP Q56187 EXPRESSION TAG SEQADV 3QUR ARG A -3 UNP Q56187 EXPRESSION TAG SEQADV 3QUR GLY A -2 UNP Q56187 EXPRESSION TAG SEQADV 3QUR SER A -1 UNP Q56187 EXPRESSION TAG SEQADV 3QUR HIS A 0 UNP Q56187 EXPRESSION TAG SEQADV 3QUR ARG A 31 UNP Q56187 PRO 31 SEE REMARK 999 SEQRES 1 A 286 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 286 LEU VAL PRO ARG GLY SER HIS MET THR PRO ASP PHE LEU SEQRES 3 A 286 ALA ILE LYS VAL GLY GLY SER LEU PHE SER ARG LYS ASP SEQRES 4 A 286 GLU PRO GLY SER LEU ASP ASP ASP ALA VAL THR ARG PHE SEQRES 5 A 286 ALA ARG ASN PHE ALA ARG LEU ALA GLU THR TYR ARG GLY SEQRES 6 A 286 ARG MET VAL LEU ILE SER GLY GLY GLY ALA PHE GLY HIS SEQRES 7 A 286 GLY ALA ILE ARG ASP HIS ASP SER THR HIS ALA PHE SER SEQRES 8 A 286 LEU ALA GLY LEU THR GLU ALA THR PHE GLU VAL LYS LYS SEQRES 9 A 286 ARG TRP ALA GLU LYS LEU ARG GLY ILE GLY VAL ASP ALA SEQRES 10 A 286 PHE PRO LEU GLN LEU ALA ALA MET CYS THR LEU ARG ASN SEQRES 11 A 286 GLY ILE PRO GLN LEU ARG SER GLU VAL LEU ARG ASP VAL SEQRES 12 A 286 LEU ASP HIS GLY ALA LEU PRO VAL LEU ALA GLY ASP ALA SEQRES 13 A 286 LEU PHE ASP GLU HIS GLY LYS LEU TRP ALA PHE SER SER SEQRES 14 A 286 ASP ARG VAL PRO GLU VAL LEU LEU PRO MET VAL GLU GLY SEQRES 15 A 286 ARG LEU ARG VAL VAL THR LEU THR ASP VAL ASP GLY ILE SEQRES 16 A 286 VAL THR ASP GLY ALA GLY GLY ASP THR ILE LEU PRO GLU SEQRES 17 A 286 VAL ASP ALA ARG SER PRO GLU GLN ALA TYR ALA ALA LEU SEQRES 18 A 286 TRP GLY SER SER GLU TRP ASP ALA THR GLY ALA MET HIS SEQRES 19 A 286 THR LYS LEU ASP ALA LEU VAL THR CYS ALA ARG ARG GLY SEQRES 20 A 286 ALA GLU CYS PHE ILE MET ARG GLY ASP PRO GLY SER ASP SEQRES 21 A 286 LEU GLU PHE LEU THR ALA PRO PHE SER SER TRP PRO ALA SEQRES 22 A 286 HIS VAL ARG SER THR ARG ILE THR THR THR ALA SER ALA HET ADP A1260 27 HET FM4 A2000 12 HET MG A3000 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM FM4 [(2R,3S)-3-METHYLOXIRAN-2-YL]-PHOSPHONOOXY-PHOSPHINIC HETNAM 2 FM4 ACID HETNAM MG MAGNESIUM ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 FM4 C3 H8 O7 P2 FORMUL 4 MG MG 2+ FORMUL 5 HOH *232(H2 O) HELIX 1 1 GLY A 12 LEU A 14 5 3 HELIX 2 2 ASP A 25 TYR A 43 1 19 HELIX 3 3 ALA A 69 SER A 71 5 3 HELIX 4 4 LEU A 72 ILE A 93 1 22 HELIX 5 5 GLN A 101 ALA A 104 5 4 HELIX 6 6 GLU A 118 HIS A 126 1 9 HELIX 7 7 SER A 148 ASP A 150 5 3 HELIX 8 8 ARG A 151 LEU A 157 1 7 HELIX 9 9 PRO A 194 SER A 204 1 11 HELIX 10 10 GLY A 211 ARG A 226 1 16 HELIX 11 11 LEU A 241 ALA A 246 5 6 HELIX 12 12 PRO A 247 TRP A 251 5 5 SHEET 1 A 8 ALA A 97 PRO A 99 0 SHEET 2 A 8 LEU A 129 ALA A 133 1 O LEU A 129 N PHE A 98 SHEET 3 A 8 MET A 47 SER A 51 1 N LEU A 49 O LEU A 132 SHEET 4 A 8 PHE A 5 VAL A 10 1 N ILE A 8 O ILE A 50 SHEET 5 A 8 LEU A 164 THR A 170 1 O LEU A 169 N LYS A 9 SHEET 6 A 8 GLU A 229 ARG A 234 1 O PHE A 231 N THR A 168 SHEET 7 A 8 SER A 257 THR A 261 -1 O ILE A 260 N CYS A 230 SHEET 8 A 8 GLU A 188 ASP A 190 1 N VAL A 189 O ARG A 259 SHEET 1 B 2 SER A 16 ARG A 17 0 SHEET 2 B 2 GLU A 20 LEU A 24 -1 O GLU A 20 N ARG A 17 SHEET 1 C 2 CYS A 106 ARG A 109 0 SHEET 2 C 2 ILE A 112 LEU A 115 -1 O GLN A 114 N THR A 107 SHEET 1 D 2 ASP A 135 PHE A 138 0 SHEET 2 D 2 LEU A 144 PHE A 147 -1 O PHE A 147 N ASP A 135 SHEET 1 E 2 VAL A 176 THR A 177 0 SHEET 2 E 2 THR A 184 ILE A 185 -1 O THR A 184 N THR A 177 LINK O HOH A 435 MG MG A3000 1555 1555 2.07 LINK O2A ADP A1260 MG MG A3000 1555 1555 2.17 LINK O1B ADP A1260 MG MG A3000 1555 1555 2.67 LINK O2 FM4 A2000 MG MG A3000 1555 1555 2.19 SITE 1 AC1 25 LYS A 9 GLY A 11 GLY A 12 SER A 13 SITE 2 AC1 25 THR A 170 ASP A 171 VAL A 172 GLY A 174 SITE 3 AC1 25 ILE A 175 VAL A 176 ALA A 200 LEU A 201 SITE 4 AC1 25 SER A 204 SER A 205 ALA A 212 MET A 213 SITE 5 AC1 25 LYS A 216 HOH A 281 HOH A 286 HOH A 319 SITE 6 AC1 25 HOH A 416 HOH A 438 HOH A 470 FM4 A2000 SITE 7 AC1 25 MG A3000 SITE 1 AC2 14 LYS A 9 GLY A 11 GLY A 12 GLY A 52 SITE 2 AC2 14 GLY A 53 PHE A 147 SER A 148 SER A 149 SITE 3 AC2 14 HOH A 305 HOH A 350 HOH A 435 HOH A 470 SITE 4 AC2 14 ADP A1260 MG A3000 SITE 1 AC3 6 ASP A 150 ALA A 212 LYS A 216 HOH A 435 SITE 2 AC3 6 ADP A1260 FM4 A2000 CRYST1 87.910 87.910 79.230 90.00 90.00 120.00 P 32 2 1 6 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 0.011375 0.006568 0.000000 0.00000 SCALE2 0.000000 0.013135 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012621 0.00000