HEADER LYASE 13-JUL-16 5GME TITLE CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS DIPHOSPHOMEVALONATE TITLE 2 DECARBOXYLASE IN COMPLEX WITH ADP 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, ADP, KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR H.UNNO,H.HEMMI,A.HATTORI REVDAT 4 08-NOV-23 5GME 1 REMARK REVDAT 3 26-FEB-20 5GME 1 REMARK REVDAT 2 22-FEB-17 5GME 1 JRNL REVDAT 1 28-DEC-16 5GME 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. 1.70 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 47643 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2551 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3503 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 190 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2597 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 257 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.58 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) : 0.01000 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): 0.084 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.607 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 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): 2724 ; 0.026 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2604 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3680 ; 2.593 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6009 ; 1.256 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 323 ; 7.169 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;34.425 ;23.950 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 505 ;15.910 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;19.172 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 406 ; 0.185 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2959 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 605 ; 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): 1295 ; 2.953 ; 2.433 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1294 ; 2.933 ; 2.430 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1617 ; 3.821 ; 3.637 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1618 ; 3.825 ; 3.640 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1427 ; 4.422 ; 3.030 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1420 ; 4.417 ; 3.031 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2052 ; 6.621 ; 4.332 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3348 ; 8.630 ;21.136 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3224 ; 8.595 ;20.639 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 : 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 5GME 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_1300000410. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-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 : 50337 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 27.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 15.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.0000 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 (%): 60.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 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 75.64450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.67337 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 34.80733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 75.64450 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 43.67337 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 34.80733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 75.64450 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 43.67337 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 34.80733 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 75.64450 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 43.67337 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.80733 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 75.64450 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 43.67337 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 34.80733 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 75.64450 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 43.67337 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 34.80733 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 87.34674 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 69.61467 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 87.34674 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 69.61467 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 87.34674 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 69.61467 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 87.34674 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 69.61467 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 87.34674 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 69.61467 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 87.34674 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 69.61467 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: 6630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 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 1 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 1179 O HOH A 1239 1.18 REMARK 500 O HOH A 1313 O HOH A 1351 1.28 REMARK 500 O HOH A 1104 O HOH A 1319 1.37 REMARK 500 O HOH A 1278 O HOH A 1325 1.63 REMARK 500 O HOH A 1291 O HOH A 1325 1.63 REMARK 500 O HOH A 1173 O HOH A 1236 1.66 REMARK 500 O HOH A 1205 O HOH A 1291 1.67 REMARK 500 O HOH A 1227 O HOH A 1305 1.78 REMARK 500 O HOH A 1149 O HOH A 1282 1.82 REMARK 500 CB SER A 44 O HOH A 1112 1.86 REMARK 500 O HOH A 1116 O HOH A 1217 1.88 REMARK 500 O1A DP6 A 1001 O HOH A 1101 1.90 REMARK 500 O HOH A 1111 O HOH A 1164 1.99 REMARK 500 OE1 GLU A 224 O HOH A 1102 2.02 REMARK 500 O HOH A 1101 O HOH A 1131 2.08 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 1295 O HOH A 1314 4555 1.58 REMARK 500 O HOH A 1235 O HOH A 1301 4555 1.83 REMARK 500 O HOH A 1248 O HOH A 1248 4555 1.93 REMARK 500 O HOH A 1164 O HOH A 1279 3555 2.03 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 -0.140 REMARK 500 CYS A 143 CA CYS A 143 CB -0.079 REMARK 500 MET A 198 CB MET A 198 CG -0.200 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 VAL A 7 CG1 - CB - CG2 ANGL. DEV. = 11.2 DEGREES REMARK 500 ARG A 158 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 GLU A 159 OE1 - CD - OE2 ANGL. DEV. = -9.2 DEGREES REMARK 500 ASP A 173 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 MET A 198 CB - CA - C ANGL. DEV. = -14.0 DEGREES REMARK 500 MET A 198 CG - SD - CE ANGL. DEV. = -18.8 DEGREES REMARK 500 GLU A 206 OE1 - CD - OE2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG A 211 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 265 NE - CZ - NH1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 265 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 293 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 LEU A 305 CB - CG - CD1 ANGL. DEV. = 15.3 DEGREES REMARK 500 ARG A 309 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 309 NE - CZ - NH2 ANGL. DEV. = -5.7 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 37.25 21.43 REMARK 500 GLU A 66 -13.28 -35.89 REMARK 500 MET A 69 -1.69 -45.99 REMARK 500 LYS A 70 -135.88 -89.17 REMARK 500 GLU A 71 3.31 -18.25 REMARK 500 TYR A 72 -97.18 -131.82 REMARK 500 ASP A 281 -145.67 -83.88 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 GLU A 68 MET A 69 149.72 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 ADP 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: 5GMD RELATED DB: PDB DBREF 5GME 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 ADP A1002 27 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 ADP ADENOSINE-5'-DIPHOSPHATE HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 2 DP6 C6 H14 O10 P2 FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 AMP C10 H14 N5 O7 P FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 HOH *257(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 TYR A 72 GLY A 85 1 14 HELIX 4 AA4 PHE A 98 ALA A 102 5 5 HELIX 5 AA5 SER A 107 LEU A 122 1 16 HELIX 6 AA6 LYS A 127 SER A 139 1 13 HELIX 7 AA7 GLY A 140 PHE A 147 5 8 HELIX 8 AA8 SER A 193 SER A 205 1 13 HELIX 9 AA9 LEU A 207 ASN A 228 1 22 HELIX 10 AB1 ASP A 230 ASP A 251 1 22 HELIX 11 AB2 ASN A 260 GLY A 274 1 15 HELIX 12 AB3 ASN A 294 LYS A 303 1 10 HELIX 13 AB4 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 THR A 50 O LYS A 91 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 TRP A 153 N SER A 34 SHEET 4 AA2 4 TYR A 165 PHE A 170 -1 O TYR A 167 N VAL A 152 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 2.38 CISPEP 1 TRP A 253 PRO A 254 0 -6.58 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 HOH A1101 HOH A1131 HOH A1134 SITE 5 AC1 18 HOH A1190 HOH A1198 SITE 1 AC2 15 LEU A 64 GLU A 68 TYR A 72 SER A 94 SITE 2 AC2 15 SER A 106 SER A 107 GLY A 110 LYS A 190 SITE 3 AC2 15 HOH A1101 HOH A1131 HOH A1141 HOH A1174 SITE 4 AC2 15 HOH A1198 HOH A1214 HOH A1215 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 A1103 SITE 3 AC3 13 HOH A1109 HOH A1226 HOH A1231 HOH A1260 SITE 4 AC3 13 HOH A1279 SITE 1 AC4 2 ARG A 158 ASP A 163 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 A1237 CRYST1 151.289 151.289 104.422 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 0.006610 0.003816 0.000000 0.00000 SCALE2 0.000000 0.007632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009577 0.00000