HEADER ONCOPROTEIN 08-FEB-16 5B30 TITLE H-RAS WT IN COMPLEX WITH GPPNHP (STATE 1) AFTER STRUCTURAL TRANSITION TITLE 2 BY HUMIDITY CONTROL COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE HRAS; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: H-RAS-1,HA-RAS,TRANSFORMING PROTEIN P21,C-H-RAS,P21RAS; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HRAS, HRAS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS ONCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.KUMASAKA,N.MIYANO,S.BABA,S.MATSUMOTO,T.KATAOKA,F.SHIMA REVDAT 3 08-NOV-23 5B30 1 LINK REVDAT 2 26-FEB-20 5B30 1 REMARK REVDAT 1 01-JUN-16 5B30 0 JRNL AUTH S.MATSUMOTO,N.MIYANO,S.BABA,J.LIAO,T.KAWAMURA,C.TSUDA, JRNL AUTH 2 A.TAKEDA,M.YAMAMOTO,T.KUMASAKA,T.KATAOKA,F.SHIMA JRNL TITL MOLECULAR MECHANISM FOR CONFORMATIONAL DYNAMICS OF RAS-GTP JRNL TITL 2 ELUCIDATED FROM IN-SITU STRUCTURAL TRANSITION IN CRYSTAL JRNL REF SCI REP V. 6 25931 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27180801 JRNL DOI 10.1038/SREP25931 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 24764 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1328 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1777 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1317 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 163 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.06000 REMARK 3 B12 (A**2) : 0.01000 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): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.465 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1511 ; 0.027 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1387 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2044 ; 2.404 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3204 ; 1.191 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 193 ; 6.034 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;42.311 ;24.744 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 273 ;14.116 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;19.508 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 222 ; 0.158 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1739 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 348 ; 0.003 ; 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): 714 ; 2.515 ; 2.042 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 709 ; 2.354 ; 2.038 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 899 ; 3.421 ; 3.051 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 900 ; 3.426 ; 3.054 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 793 ; 3.623 ; 2.448 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 788 ; 3.560 ; 2.450 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1132 ; 5.259 ; 3.543 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1855 ; 7.060 ;18.190 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1782 ; 6.848 ;17.614 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 5B30 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1300000444. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26298 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.82300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3K8Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400, SODIUM ACETATE, CALCIUM REMARK 280 ACETATE, MAGNESIUM CHLORIDE, PH 4.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 45.89550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.49778 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 40.47233 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 45.89550 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 26.49778 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 40.47233 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 45.89550 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 26.49778 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 40.47233 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 45.89550 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 26.49778 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 40.47233 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 45.89550 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 26.49778 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 40.47233 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 45.89550 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 26.49778 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 40.47233 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 52.99556 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 80.94467 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 52.99556 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 80.94467 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 52.99556 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 80.94467 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 52.99556 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 80.94467 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 52.99556 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 80.94467 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 52.99556 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 80.94467 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CA CA A 203 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 313 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 373 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 457 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 128 CZ NH1 NH2 REMARK 470 ARG A 135 CZ NH1 NH2 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 OD1 ASP A 105 O HOH A 301 1.40 REMARK 500 OH TYR A 32 O HOH A 302 1.63 REMARK 500 O HOH A 318 O HOH A 365 1.94 REMARK 500 O HOH A 315 O HOH A 438 2.13 REMARK 500 O HOH A 387 O HOH A 442 2.14 REMARK 500 OE1 GLN A 165 O HOH A 304 2.18 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 NE2 GLN A 25 NE2 GLN A 25 18444 1.01 REMARK 500 O HOH A 304 O HOH A 395 11444 1.80 REMARK 500 CD GLN A 25 NE2 GLN A 25 18444 1.85 REMARK 500 OE1 GLN A 25 OE1 GLN A 25 18444 2.10 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 ARG A 97 CZ ARG A 97 NH2 -0.124 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 33 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 MET A 72 CA - CB - CG ANGL. DEV. = 12.0 DEGREES REMARK 500 ARG A 73 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 73 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 102 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ASP A 105 CB - CG - OD2 ANGL. DEV. = 9.0 DEGREES REMARK 500 MET A 111 CG - SD - CE ANGL. DEV. = -11.6 DEGREES REMARK 500 ARG A 123 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 132 CB - CG - OD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 TYR A 157 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 161 NE - CZ - NH2 ANGL. DEV. = -3.2 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 ARG A 149 -5.50 79.85 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 GNP A 201 O2G 170.8 REMARK 620 3 GNP A 201 O2B 83.4 92.1 REMARK 620 4 HOH A 319 O 82.4 89.4 87.2 REMARK 620 5 HOH A 344 O 89.9 97.8 86.9 170.7 REMARK 620 6 HOH A 432 O 91.3 93.4 174.5 93.3 92.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 204 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 102 O REMARK 620 2 ARG A 102 O 0.0 REMARK 620 3 ASP A 105 OD2 91.2 91.2 REMARK 620 4 ASP A 105 OD1 100.8 100.8 57.2 REMARK 620 5 ASP A 105 OD2 91.2 91.2 0.0 57.2 REMARK 620 6 HOH A 301 O 96.5 96.5 90.4 33.6 90.4 REMARK 620 7 HOH A 426 O 88.2 88.2 155.8 99.2 155.8 65.7 REMARK 620 8 HOH A 426 O 89.7 89.7 174.5 117.4 174.5 84.2 18.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 107 O REMARK 620 2 TYR A 137 O 154.4 REMARK 620 3 HOH A 349 O 100.3 99.6 REMARK 620 4 HOH A 403 O 80.1 82.6 94.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 327 O REMARK 620 2 HOH A 327 O 30.3 REMARK 620 3 HOH A 368 O 133.0 113.5 REMARK 620 4 HOH A 368 O 113.8 143.3 87.2 REMARK 620 5 HOH A 399 O 65.8 73.8 76.7 82.7 REMARK 620 6 HOH A 399 O 71.4 91.6 154.6 73.7 116.1 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 GNP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5B2Z RELATED DB: PDB DBREF 5B30 A 1 166 UNP P01112 RASH_HUMAN 1 166 SEQADV 5B30 GLY A -4 UNP P01112 EXPRESSION TAG SEQADV 5B30 PRO A -3 UNP P01112 EXPRESSION TAG SEQADV 5B30 LEU A -2 UNP P01112 EXPRESSION TAG SEQADV 5B30 GLY A -1 UNP P01112 EXPRESSION TAG SEQADV 5B30 SER A 0 UNP P01112 EXPRESSION TAG SEQRES 1 A 171 GLY PRO LEU GLY SER MET THR GLU TYR LYS LEU VAL VAL SEQRES 2 A 171 VAL GLY ALA GLY GLY VAL GLY LYS SER ALA LEU THR ILE SEQRES 3 A 171 GLN LEU ILE GLN ASN HIS PHE VAL ASP GLU TYR ASP PRO SEQRES 4 A 171 THR ILE GLU ASP SER TYR ARG LYS GLN VAL VAL ILE ASP SEQRES 5 A 171 GLY GLU THR CYS LEU LEU ASP ILE LEU ASP THR ALA GLY SEQRES 6 A 171 GLN GLU GLU TYR SER ALA MET ARG ASP GLN TYR MET ARG SEQRES 7 A 171 THR GLY GLU GLY PHE LEU CYS VAL PHE ALA ILE ASN ASN SEQRES 8 A 171 THR LYS SER PHE GLU ASP ILE HIS GLN TYR ARG GLU GLN SEQRES 9 A 171 ILE LYS ARG VAL LYS ASP SER ASP ASP VAL PRO MET VAL SEQRES 10 A 171 LEU VAL GLY ASN LYS CYS ASP LEU ALA ALA ARG THR VAL SEQRES 11 A 171 GLU SER ARG GLN ALA GLN ASP LEU ALA ARG SER TYR GLY SEQRES 12 A 171 ILE PRO TYR ILE GLU THR SER ALA LYS THR ARG GLN GLY SEQRES 13 A 171 VAL GLU ASP ALA PHE TYR THR LEU VAL ARG GLU ILE ARG SEQRES 14 A 171 GLN HIS HET GNP A 201 32 HET MG A 202 1 HET CA A 203 1 HET CA A 204 1 HET NA A 205 1 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 2 GNP C10 H17 N6 O13 P3 FORMUL 3 MG MG 2+ FORMUL 4 CA 2(CA 2+) FORMUL 6 NA NA 1+ FORMUL 7 HOH *163(H2 O) HELIX 1 AA1 GLY A 15 ASN A 26 1 12 HELIX 2 AA2 SER A 65 ARG A 73 1 9 HELIX 3 AA3 ASN A 86 ASP A 92 1 7 HELIX 4 AA4 ASP A 92 ASP A 105 1 14 HELIX 5 AA5 GLU A 126 GLY A 138 1 13 HELIX 6 AA6 GLY A 151 ARG A 164 1 14 SHEET 1 AA1 6 SER A 39 ILE A 46 0 SHEET 2 AA1 6 GLU A 49 ASP A 57 -1 O LEU A 53 N LYS A 42 SHEET 3 AA1 6 THR A 2 GLY A 10 1 N VAL A 8 O LEU A 56 SHEET 4 AA1 6 GLY A 77 ALA A 83 1 O VAL A 81 N VAL A 9 SHEET 5 AA1 6 MET A 111 ASN A 116 1 O ASN A 116 N PHE A 82 SHEET 6 AA1 6 TYR A 141 GLU A 143 1 O ILE A 142 N LEU A 113 LINK OG SER A 17 MG MG A 202 1555 1555 2.25 LINK O ARG A 102 CA CA A 204 1555 1555 2.31 LINK O ARG A 102 CA CA A 204 1555 16544 2.29 LINK OD2 ASP A 105 CA CA A 204 1555 1555 2.38 LINK OD1 ASP A 105 CA CA A 204 1555 16544 2.55 LINK OD2 ASP A 105 CA CA A 204 1555 16544 2.91 LINK O ASP A 107 NA NA A 205 1555 1555 2.24 LINK O TYR A 137 NA NA A 205 1555 1555 2.37 LINK O2G GNP A 201 MG MG A 202 1555 1555 2.17 LINK O2B GNP A 201 MG MG A 202 1555 1555 2.26 LINK MG MG A 202 O HOH A 319 1555 1555 2.30 LINK MG MG A 202 O HOH A 344 1555 1555 2.22 LINK MG MG A 202 O HOH A 432 1555 1555 2.22 LINK CA CA A 203 O HOH A 327 1555 1555 2.38 LINK CA CA A 203 O HOH A 327 1555 3555 2.39 LINK CA CA A 203 O HOH A 368 1555 1555 2.33 LINK CA CA A 203 O HOH A 368 1555 2555 2.34 LINK CA CA A 203 O HOH A 399 1555 1555 2.32 LINK CA CA A 203 O HOH A 399 1555 2555 2.48 LINK CA CA A 204 O HOH A 301 1555 1555 2.43 LINK CA CA A 204 O HOH A 426 1555 1555 2.34 LINK CA CA A 204 O HOH A 426 1555 16544 2.49 LINK NA NA A 205 O HOH A 349 1555 1555 2.27 LINK NA NA A 205 O HOH A 403 1555 1555 2.28 SITE 1 AC1 30 GLY A 12 GLY A 13 VAL A 14 GLY A 15 SITE 2 AC1 30 LYS A 16 SER A 17 ALA A 18 PHE A 28 SITE 3 AC1 30 VAL A 29 ASP A 30 GLU A 31 TYR A 32 SITE 4 AC1 30 ALA A 59 GLY A 60 ASN A 116 LYS A 117 SITE 5 AC1 30 ASP A 119 LEU A 120 SER A 145 ALA A 146 SITE 6 AC1 30 LYS A 147 MG A 202 HOH A 302 HOH A 344 SITE 7 AC1 30 HOH A 351 HOH A 360 HOH A 366 HOH A 387 SITE 8 AC1 30 HOH A 423 HOH A 428 SITE 1 AC2 5 SER A 17 GNP A 201 HOH A 319 HOH A 344 SITE 2 AC2 5 HOH A 432 SITE 1 AC3 3 HOH A 327 HOH A 368 HOH A 399 SITE 1 AC4 4 ARG A 102 ASP A 105 HOH A 301 HOH A 426 SITE 1 AC5 5 ARG A 97 ASP A 107 TYR A 137 HOH A 349 SITE 2 AC5 5 HOH A 403 CRYST1 91.791 91.791 121.417 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 0.010894 0.006290 0.000000 0.00000 SCALE2 0.000000 0.012580 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008236 0.00000