HEADER LYASE 13-JUL-16 5GMD TITLE CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS DIPHOSPHOMEVALONATE TITLE 2 DECARBOXYLASE IN COMPLEX WITH ATP-GAMMA-S COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPHOSPHOMEVALONATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DMD; COMPND 5 EC: 4.1.1.33; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS (STRAIN ATCC 35092 / SOURCE 3 DSM 1617 / JCM 11322 / P2); SOURCE 4 ORGANISM_TAXID: 273057; SOURCE 5 STRAIN: ATCC 35092 / DSM 1617 / JCM 11322 / P2; SOURCE 6 GENE: SSO2989; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS SULFOLOBUS SOLFATARICUS, DIPHOSPHOMEVALONATE DECARBOXYLASE, ATPRS, KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR H.UNNO,H.HEMMI,A.HATTORI REVDAT 4 08-NOV-23 5GMD 1 REMARK REVDAT 3 26-FEB-20 5GMD 1 REMARK REVDAT 2 22-FEB-17 5GMD 1 JRNL REVDAT 1 28-DEC-16 5GMD 0 JRNL AUTH K.MOTOYAMA,H.UNNO,A.HATTORI,T.TAKAOKA,H.ISHIKITA,H.KAWAIDE, JRNL AUTH 2 T.YOSHIMURA,H.HEMMI JRNL TITL A SINGLE AMINO ACID MUTATION CONVERTS JRNL TITL 2 (R)-5-DIPHOSPHOMEVALONATE DECARBOXYLASE INTO A KINASE JRNL REF J. BIOL. CHEM. V. 292 2457 2017 JRNL REFN ESSN 1083-351X JRNL PMID 28003359 JRNL DOI 10.1074/JBC.M116.752535 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 68482 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3638 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5042 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE SET COUNT : 290 REMARK 3 BIN FREE R VALUE : 0.2230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2605 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 82 REMARK 3 SOLVENT ATOMS : 243 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.057 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.061 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.869 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2747 ; 0.031 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2621 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3715 ; 2.956 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6053 ; 1.360 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 6.523 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;35.189 ;24.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 511 ;14.315 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.759 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 410 ; 0.230 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2984 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 608 ; 0.002 ; 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): 1303 ; 2.407 ; 1.703 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1302 ; 2.396 ; 1.702 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1628 ; 3.265 ; 2.551 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1629 ; 3.268 ; 2.552 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1442 ; 4.558 ; 2.261 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1435 ; 4.499 ; 2.256 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2074 ; 6.513 ; 3.203 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3378 ; 9.708 ;15.489 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3259 ; 9.667 ;15.082 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5GMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1300000411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72082 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 48.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4Z7C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 1.5M AMMONIUM REMARK 280 SULFATE, PH 4.6, VAPOR DIFFUSION, 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 75.61900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.65865 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 34.80533 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 75.61900 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 43.65865 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 34.80533 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 75.61900 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 43.65865 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 34.80533 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 75.61900 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 43.65865 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.80533 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 75.61900 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 43.65865 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 34.80533 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 75.61900 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 43.65865 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 34.80533 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 87.31730 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 69.61067 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 87.31730 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 69.61067 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 87.31730 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 69.61067 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 87.31730 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 69.61067 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 87.31730 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 69.61067 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 87.31730 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 69.61067 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: 7290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -128.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1262 O HOH A 1264 1.01 REMARK 500 O HOH A 1110 O HOH A 1177 1.47 REMARK 500 OE1 GLU A 25 O HOH A 1101 1.49 REMARK 500 O HOH A 1123 O HOH A 1229 1.61 REMARK 500 O HOH A 1118 O HOH A 1240 1.66 REMARK 500 O HOH A 1254 O HOH A 1311 1.71 REMARK 500 O HOH A 1153 O HOH A 1171 1.72 REMARK 500 CB SER A 44 O HOH A 1133 1.75 REMARK 500 O HOH A 1180 O HOH A 1280 1.83 REMARK 500 O HOH A 1191 O HOH A 1275 1.86 REMARK 500 O2G AGS A 1002 O HOH A 1102 2.03 REMARK 500 OE1 GLU A 203 O HOH A 1103 2.11 REMARK 500 NZ LYS A 190 O3G AGS A 1002 2.17 REMARK 500 O HOH A 1105 O HOH A 1246 2.19 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 1210 O HOH A 1210 4555 1.87 REMARK 500 O HOH A 1298 O HOH A 1324 4555 2.06 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 SER A 34 CB SER A 34 OG -0.131 REMARK 500 SER A 128 CB SER A 128 OG 0.088 REMARK 500 GLU A 129 CD GLU A 129 OE1 -0.088 REMARK 500 ARG A 144 CZ ARG A 144 NH1 0.085 REMARK 500 TYR A 167 CE1 TYR A 167 CZ -0.080 REMARK 500 ASP A 173 CB ASP A 173 CG 0.136 REMARK 500 SER A 176 CB SER A 176 OG -0.082 REMARK 500 ASP A 317 CB ASP A 317 CG -0.141 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 ASP A 24 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 26 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 ASP A 40 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP A 41 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 LEU A 121 CB - CG - CD1 ANGL. DEV. = 11.0 DEGREES REMARK 500 LYS A 127 CD - CE - NZ ANGL. DEV. = 19.0 DEGREES REMARK 500 ARG A 136 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 144 CD - NE - CZ ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 144 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 PHE A 147 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 158 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 GLU A 159 OE1 - CD - OE2 ANGL. DEV. = -9.1 DEGREES REMARK 500 ARG A 171 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP A 173 CB - CG - OD2 ANGL. DEV. = 11.1 DEGREES REMARK 500 GLU A 206 OE1 - CD - OE2 ANGL. DEV. = -11.2 DEGREES REMARK 500 ARG A 211 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 211 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 227 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 229 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 229 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 230 CB - CG - OD1 ANGL. DEV. = 11.5 DEGREES REMARK 500 TYR A 235 CD1 - CE1 - CZ ANGL. DEV. = -5.7 DEGREES REMARK 500 PHE A 257 CB - CG - CD2 ANGL. DEV. = 4.9 DEGREES REMARK 500 ASP A 261 OD1 - CG - OD2 ANGL. DEV. = 12.6 DEGREES REMARK 500 ASP A 261 CB - CG - OD2 ANGL. DEV. = -11.5 DEGREES REMARK 500 ASP A 281 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 GLU A 292 OE1 - CD - OE2 ANGL. DEV. = -9.9 DEGREES REMARK 500 LEU A 305 CB - CG - CD1 ANGL. DEV. = 15.2 DEGREES REMARK 500 ASP A 317 CB - CG - OD1 ANGL. DEV. = 8.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 61 26.48 36.38 REMARK 500 TYR A 72 -100.07 -127.53 REMARK 500 ASP A 281 -148.72 -87.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DP6 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AGS A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1005 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GME RELATED DB: PDB DBREF 5GMD A 1 325 UNP Q97UL5 DMD_SULSO 1 325 SEQRES 1 A 325 MET LEU LYS SER VAL THR VAL SER ALA PRO SER ASN ILE SEQRES 2 A 325 ALA VAL VAL LYS TYR TRP GLY LYS ARG GLY ASP GLU ARG SEQRES 3 A 325 LEU ASN LEU PRO LEU ASN ASN SER LEU SER ILE THR LEU SEQRES 4 A 325 ASP ASP GLN LEU SER VAL ILE THR LYS VAL THR LEU ASN SEQRES 5 A 325 ASP LYS ASN ILE VAL ILE VAL ASN ASP ARG ILE LEU SER SEQRES 6 A 325 GLU ASP GLU MET LYS GLU TYR ALA GLY ARG VAL LEU ASP SEQRES 7 A 325 THR PHE LYS LYS ILE VAL GLY LYS GLU PHE HIS VAL LYS SEQRES 8 A 325 VAL GLU SER LYS SER LYS PHE PRO ILE ASN ALA GLY LEU SEQRES 9 A 325 ALA SER SER ALA ALA GLY ILE ALA ALA LEU ALA PHE SER SEQRES 10 A 325 LEU ASN GLU LEU LEU GLU LEU ASN LEU LYS SER GLU GLU SEQRES 11 A 325 LEU SER LYS ILE ALA ARG LEU GLY SER GLY SER ALA CYS SEQRES 12 A 325 ARG SER MET PHE GLY GLY PHE VAL VAL TRP ASN LYS GLY SEQRES 13 A 325 GLU ARG GLU ASP GLY GLU ASP SER TYR CYS TYR GLN ILE SEQRES 14 A 325 PHE ARG HIS ASP TYR TRP SER GLU LEU VAL ASP ILE ILE SEQRES 15 A 325 PRO ILE LEU SER GLU LYS GLU LYS LYS ILE SER SER ARG SEQRES 16 A 325 LYS GLY MET ILE ARG SER ALA GLU THR SER GLU LEU MET SEQRES 17 A 325 GLU CYS ARG LEU LYS TYR ILE GLU LYS THR PHE ASN GLU SEQRES 18 A 325 VAL ILE GLU ALA ILE ARG ASN ARG ASP GLU LYS LYS PHE SEQRES 19 A 325 TYR TYR LEU MET MET ARG HIS SER ASN SER MET HIS ALA SEQRES 20 A 325 VAL ILE LEU ASP SER TRP PRO SER PHE PHE TYR LEU ASN SEQRES 21 A 325 ASP THR SER ILE ARG ILE MET GLU TRP ILE HIS ASP TYR SEQRES 22 A 325 GLY LYS ALA GLY TYR THR PHE ASP ALA GLY PRO ASN PRO SEQRES 23 A 325 HIS ILE PHE THR THR GLU ARG ASN ILE GLY ASP ILE LEU SEQRES 24 A 325 GLU PHE LEU LYS SER LEU GLU ILE LYS ARG ILE ILE VAL SEQRES 25 A 325 SER LYS VAL GLY ASP GLY PRO LYS VAL LEU SER ARG GLU HET DP6 A1001 18 HET AGS A1002 31 HET AMP A1003 23 HET SO4 A1004 5 HET SO4 A1005 5 HETNAM DP6 (3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 DP6 PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID HETNAM AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM SO4 SULFATE ION HETSYN AGS ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); HETSYN 2 AGS ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'- HETSYN 3 AGS DIPHOSPHATE MONOTHIOPHOSPHATE FORMUL 2 DP6 C6 H14 O10 P2 FORMUL 3 AGS C10 H16 N5 O12 P3 S FORMUL 4 AMP C10 H14 N5 O7 P FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 HOH *243(H2 O) HELIX 1 AA1 ASP A 24 ASN A 28 5 5 HELIX 2 AA2 ASP A 40 LEU A 43 5 4 HELIX 3 AA3 SER A 65 LYS A 70 1 6 HELIX 4 AA4 TYR A 72 GLY A 85 1 14 HELIX 5 AA5 PHE A 98 ALA A 102 5 5 HELIX 6 AA6 SER A 107 LEU A 122 1 16 HELIX 7 AA7 LYS A 127 SER A 139 1 13 HELIX 8 AA8 GLY A 140 PHE A 147 5 8 HELIX 9 AA9 SER A 193 SER A 205 1 13 HELIX 10 AB1 LEU A 207 ASN A 228 1 22 HELIX 11 AB2 ASP A 230 ASP A 251 1 22 HELIX 12 AB3 ASN A 260 GLY A 274 1 15 HELIX 13 AB4 ASN A 294 LYS A 303 1 10 HELIX 14 AB5 SER A 304 GLU A 306 5 3 SHEET 1 AA1 6 ARG A 62 ILE A 63 0 SHEET 2 AA1 6 ILE A 56 VAL A 59 -1 N VAL A 59 O ARG A 62 SHEET 3 AA1 6 VAL A 90 SER A 96 1 O VAL A 92 N ILE A 56 SHEET 4 AA1 6 VAL A 45 LEU A 51 -1 N LYS A 48 O GLU A 93 SHEET 5 AA1 6 SER A 4 ALA A 9 -1 N VAL A 7 O THR A 47 SHEET 6 AA1 6 LYS A 320 ARG A 324 -1 O LEU A 322 N THR A 6 SHEET 1 AA2 4 ASN A 12 VAL A 16 0 SHEET 2 AA2 4 SER A 34 THR A 38 -1 O LEU A 35 N VAL A 15 SHEET 3 AA2 4 PHE A 150 ASN A 154 -1 O VAL A 151 N SER A 36 SHEET 4 AA2 4 TYR A 165 PHE A 170 -1 O ILE A 169 N PHE A 150 SHEET 1 AA3 2 LYS A 21 ARG A 22 0 SHEET 2 AA3 2 LEU A 29 PRO A 30 -1 O LEU A 29 N ARG A 22 SHEET 1 AA4 4 GLY A 277 THR A 279 0 SHEET 2 AA4 4 HIS A 287 THR A 291 -1 O PHE A 289 N GLY A 277 SHEET 3 AA4 4 LEU A 178 PRO A 183 -1 N ILE A 181 O ILE A 288 SHEET 4 AA4 4 ILE A 310 LYS A 314 -1 O ILE A 311 N ILE A 182 SSBOND 1 CYS A 210 CYS A 210 1555 4555 2.32 CISPEP 1 TRP A 253 PRO A 254 0 -7.99 SITE 1 AC1 18 ALA A 14 LYS A 17 TYR A 18 LYS A 21 SITE 2 AC1 18 ASN A 28 SER A 139 GLY A 140 SER A 141 SITE 3 AC1 18 ARG A 144 SER A 194 ARG A 195 MET A 198 SITE 4 AC1 18 ASP A 281 AGS A1002 HOH A1131 HOH A1138 SITE 5 AC1 18 HOH A1141 HOH A1189 SITE 1 AC2 20 VAL A 59 GLU A 68 TYR A 72 SER A 94 SITE 2 AC2 20 SER A 106 SER A 107 GLY A 110 LYS A 190 SITE 3 AC2 20 SER A 194 DP6 A1001 HOH A1102 HOH A1135 SITE 4 AC2 20 HOH A1138 HOH A1141 HOH A1152 HOH A1189 SITE 5 AC2 20 HOH A1190 HOH A1226 HOH A1233 HOH A1252 SITE 1 AC3 13 ARG A 22 GLY A 23 LYS A 155 GLU A 157 SITE 2 AC3 13 GLU A 159 GLU A 216 PHE A 219 HOH A1105 SITE 3 AC3 13 HOH A1108 HOH A1232 HOH A1243 HOH A1246 SITE 4 AC3 13 HOH A1286 SITE 1 AC4 8 LEU A 104 ALA A 105 ILE A 182 ASN A 285 SITE 2 AC4 8 HIS A 287 HOH A1119 HOH A1207 HOH A1219 SITE 1 AC5 7 GLY A 148 GLN A 168 ARG A 171 HIS A 172 SITE 2 AC5 7 ASP A 317 GLY A 318 HOH A1266 CRYST1 151.238 151.238 104.416 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 0.006612 0.003817 0.000000 0.00000 SCALE2 0.000000 0.007635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009577 0.00000