HEADER TRANSFERASE 13-MAY-08 3D41 TITLE CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM TITLE 2 STREPTOMYCES WEDMORENSIS COMPLEXED WITH MGAMPPNP AND FOSFOMYCIN 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; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS FOSFOMYCIN, ANTIBIOTIC RESISTANCE, KINASE, PHOSPHORYL TRANSFER, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.PAKHOMOVA,S.G.BARTLETT,A.AUGUSTUS,T.KUZUYAMA,M.E.NEWCOMER REVDAT 6 30-AUG-23 3D41 1 REMARK SEQADV LINK REVDAT 5 13-JUL-11 3D41 1 VERSN REVDAT 4 24-FEB-09 3D41 1 VERSN REVDAT 3 28-OCT-08 3D41 1 JRNL REVDAT 2 09-SEP-08 3D41 1 JRNL REVDAT 1 12-AUG-08 3D41 0 JRNL AUTH S.PAKHOMOVA,S.G.BARTLETT,A.AUGUSTUS,T.KUZUYAMA,M.E.NEWCOMER JRNL TITL CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM JRNL TITL 2 STREPTOMYCES WEDMORENSIS. JRNL REF J.BIOL.CHEM. V. 283 28518 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18701452 JRNL DOI 10.1074/JBC.M803709200 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 15587 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.400 REMARK 3 FREE R VALUE TEST SET COUNT : 215 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : 920 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2024 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 46.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.11000 REMARK 3 B22 (A**2) : 2.11000 REMARK 3 B33 (A**2) : -3.17000 REMARK 3 B12 (A**2) : 1.06000 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): 0.242 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.213 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.174 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.560 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2121 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2885 ; 1.727 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 268 ; 7.079 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 87 ;33.522 ;21.954 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 329 ;17.794 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;21.808 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 328 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1594 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 871 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1414 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 114 ; 0.174 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.093 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 54 ; 0.203 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.239 ; 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): 1361 ; 0.712 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2135 ; 1.233 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 843 ; 1.854 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 747 ; 3.092 ; 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 69 REMARK 3 ORIGIN FOR THE GROUP (A): 24.4134 14.9881 9.3938 REMARK 3 T TENSOR REMARK 3 T11: 0.0548 T22: -0.2712 REMARK 3 T33: -0.0593 T12: 0.0923 REMARK 3 T13: 0.1243 T23: 0.1504 REMARK 3 L TENSOR REMARK 3 L11: 5.1194 L22: 4.8638 REMARK 3 L33: 6.7218 L12: -0.0384 REMARK 3 L13: 0.8461 L23: 1.6396 REMARK 3 S TENSOR REMARK 3 S11: -0.2302 S12: -0.3350 S13: -0.5399 REMARK 3 S21: -0.1789 S22: -0.1373 S23: 0.5498 REMARK 3 S31: 1.2386 S32: 0.1813 S33: 0.3675 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 70 A 263 REMARK 3 ORIGIN FOR THE GROUP (A): 30.3352 18.1422 6.3136 REMARK 3 T TENSOR REMARK 3 T11: -0.0515 T22: -0.2009 REMARK 3 T33: -0.1376 T12: 0.1130 REMARK 3 T13: 0.0744 T23: 0.0624 REMARK 3 L TENSOR REMARK 3 L11: 4.5976 L22: 1.2173 REMARK 3 L33: 4.1026 L12: -1.8236 REMARK 3 L13: 0.6130 L23: 0.0371 REMARK 3 S TENSOR REMARK 3 S11: -0.1312 S12: -0.1809 S13: -0.1403 REMARK 3 S21: 0.0223 S22: 0.0058 S23: 0.0457 REMARK 3 S31: 0.7616 S32: 0.6805 S33: 0.1254 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 : 1.20 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 3D41 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047564. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-07 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) : 1.38074 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 : 17293 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.55700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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: PDB ENTRY 3D40 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 11% PEG 3350, 0.1 M TRI-AMMONIUM REMARK 280 CITRATE, 0.1 M MES, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K 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 52.65267 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 26.32633 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 26.32633 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 52.65267 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: 5600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.7 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 GLY A 179 REMARK 465 ALA A 180 REMARK 465 GLY A 181 REMARK 465 GLY A 182 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 HIS A 68 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 178 CG OD1 OD2 REMARK 470 SER A 205 OG REMARK 470 GLU A 206 CG CD OE1 OE2 REMARK 470 TRP A 207 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 207 CZ3 CH2 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 SER A 205 N TRP A 207 2.12 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 116 NE - CZ - NH2 ANGL. DEV. = -4.5 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 -2.43 -142.90 REMARK 500 TYR A 43 57.86 -101.21 REMARK 500 LEU A 72 -12.20 -49.20 REMARK 500 SER A 193 75.05 -150.89 REMARK 500 SER A 204 164.95 -46.19 REMARK 500 GLU A 206 9.10 -40.16 REMARK 500 ALA A 212 -124.11 42.66 REMARK 500 SER A 250 42.78 -108.34 REMARK 500 PRO A 252 173.00 -59.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 204 SER A 205 147.63 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 267 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ANP A1260 O2G REMARK 620 2 ANP A1260 O2A 99.9 REMARK 620 3 ANP A1260 O1B 72.2 82.4 REMARK 620 4 HOH A4002 O 165.2 81.5 93.4 REMARK 620 5 HOH A4003 O 106.2 91.4 173.2 88.5 REMARK 620 6 HOH A4004 O 97.3 160.0 93.1 79.3 93.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 267 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A 1260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FCN A 4001 REMARK 900 REMARK 900 RELATED ENTRIES 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 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THE RESEQUENCING OF THE PROTEIN CONFIRMED REMARK 999 RESIDUE 31 IS ARG. DBREF 3D41 A 1 266 UNP Q56187 Q56187_STRWE 1 266 SEQADV 3D41 MET A -19 UNP Q56187 EXPRESSION TAG SEQADV 3D41 GLY A -18 UNP Q56187 EXPRESSION TAG SEQADV 3D41 SER A -17 UNP Q56187 EXPRESSION TAG SEQADV 3D41 SER A -16 UNP Q56187 EXPRESSION TAG SEQADV 3D41 HIS A -15 UNP Q56187 EXPRESSION TAG SEQADV 3D41 HIS A -14 UNP Q56187 EXPRESSION TAG SEQADV 3D41 HIS A -13 UNP Q56187 EXPRESSION TAG SEQADV 3D41 HIS A -12 UNP Q56187 EXPRESSION TAG SEQADV 3D41 HIS A -11 UNP Q56187 EXPRESSION TAG SEQADV 3D41 HIS A -10 UNP Q56187 EXPRESSION TAG SEQADV 3D41 SER A -9 UNP Q56187 EXPRESSION TAG SEQADV 3D41 SER A -8 UNP Q56187 EXPRESSION TAG SEQADV 3D41 GLY A -7 UNP Q56187 EXPRESSION TAG SEQADV 3D41 LEU A -6 UNP Q56187 EXPRESSION TAG SEQADV 3D41 VAL A -5 UNP Q56187 EXPRESSION TAG SEQADV 3D41 PRO A -4 UNP Q56187 EXPRESSION TAG SEQADV 3D41 ARG A -3 UNP Q56187 EXPRESSION TAG SEQADV 3D41 GLY A -2 UNP Q56187 EXPRESSION TAG SEQADV 3D41 SER A -1 UNP Q56187 EXPRESSION TAG SEQADV 3D41 HIS A 0 UNP Q56187 EXPRESSION TAG SEQADV 3D41 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 MG A 267 1 HET ANP A1260 31 HET FCN A4001 8 HETNAM MG MAGNESIUM ION HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM FCN FOSFOMYCIN HETSYN FCN 1,2-EPOXYPROPYLPHOSPHONIC ACID FORMUL 2 MG MG 2+ FORMUL 3 ANP C10 H17 N6 O12 P3 FORMUL 4 FCN C3 H7 O4 P FORMUL 5 HOH *60(H2 O) HELIX 1 1 GLY A 12 PHE A 15 5 4 HELIX 2 2 ASP A 25 TYR A 43 1 19 HELIX 3 3 GLY A 53 HIS A 64 1 12 HELIX 4 4 HIS A 68 LEU A 72 5 5 HELIX 5 5 ALA A 73 ILE A 93 1 21 HELIX 6 6 GLN A 101 ALA A 104 5 4 HELIX 7 7 GLU A 118 HIS A 126 1 9 HELIX 8 8 SER A 148 ASP A 150 5 3 HELIX 9 9 ARG A 151 LEU A 157 1 7 HELIX 10 10 PRO A 194 ALA A 200 1 7 HELIX 11 11 GLY A 211 ARG A 226 1 16 HELIX 12 12 LEU A 241 ALA A 246 5 6 HELIX 13 13 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 MET A 233 N THR A 170 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 CYS A 106 ARG A 109 0 SHEET 2 B 2 ILE A 112 LEU A 115 -1 O GLN A 114 N THR A 107 SHEET 1 C 2 ASP A 135 PHE A 138 0 SHEET 2 C 2 LEU A 144 PHE A 147 -1 O PHE A 147 N ASP A 135 SHEET 1 D 2 VAL A 176 THR A 177 0 SHEET 2 D 2 THR A 184 ILE A 185 -1 O THR A 184 N THR A 177 LINK MG MG A 267 O2G ANP A1260 1555 1555 2.16 LINK MG MG A 267 O2A ANP A1260 1555 1555 2.16 LINK MG MG A 267 O1B ANP A1260 1555 1555 2.17 LINK MG MG A 267 O HOH A4002 1555 1555 1.91 LINK MG MG A 267 O HOH A4003 1555 1555 2.05 LINK MG MG A 267 O HOH A4004 1555 1555 1.89 SITE 1 AC1 3 HOH A4002 HOH A4003 HOH A4004 SITE 1 AC2 24 LYS A 9 GLY A 11 GLY A 12 SER A 13 SITE 2 AC2 24 LYS A 18 HIS A 58 THR A 170 ASP A 171 SITE 3 AC2 24 GLY A 174 ILE A 175 ALA A 200 LEU A 201 SITE 4 AC2 24 TRP A 202 ASP A 208 ALA A 212 MET A 213 SITE 5 AC2 24 LYS A 216 HOH A4002 HOH A4003 HOH A4004 SITE 6 AC2 24 HOH A4007 HOH A4015 HOH A4031 HOH A4057 SITE 1 AC3 10 GLY A 52 GLY A 53 GLY A 57 SER A 148 SITE 2 AC3 10 SER A 149 THR A 210 HOH A4004 HOH A4010 SITE 3 AC3 10 HOH A4031 HOH A4057 CRYST1 85.656 85.656 78.979 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 0.011675 0.006740 0.000000 0.00000 SCALE2 0.000000 0.013481 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012662 0.00000