HEADER NUCLEOTIDE-BINDING PROTEIN 27-APR-06 2CLC TITLE CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN TITLE 2 COMPLEX WITH GTP (2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE HRAS; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: RESIDUES 1-166; COMPND 5 SYNONYM: H-RAS P21, TRANSFORMING PROTEIN P21, P21RAS, H-RAS-1, C-H- COMPND 6 RAS; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: AN IANBD FLUOROPHORE WAS ATTACHED TO CYS-32 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: CK600K; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTAC RAS KEYWDS NUCLEOTIDE-BINDING PROTEIN, GOLGI APPARATUS, PROTO-ONCOGENE, R-CAGED KEYWDS 2 GTP, PRENYLATION, LIPOPROTEIN, GTP-BINDING, PALMITATE, METHYLATION EXPDTA X-RAY DIFFRACTION NUMMDL 2 AUTHOR B.U.KLINK,R.S.GOODY,A.J.SCHEIDIG REVDAT 9 13-DEC-23 2CLC 1 REMARK LINK REVDAT 8 06-FEB-19 2CLC 1 REMARK REVDAT 7 30-JAN-19 2CLC 1 REMARK REVDAT 6 22-APR-15 2CLC 1 NUMMDL REMARK FORMUL SITE REVDAT 6 2 1 HETATM MASTER REVDAT 5 13-JUL-11 2CLC 1 VERSN REVDAT 4 24-FEB-09 2CLC 1 VERSN REVDAT 3 06-MAR-07 2CLC 1 COMPND KEYWDS REVDAT 2 23-AUG-06 2CLC 1 JRNL REVDAT 1 24-MAY-06 2CLC 0 JRNL AUTH B.U.KLINK,R.S.GOODY,A.J.SCHEIDIG JRNL TITL A NEWLY DESIGNED MICROSPECTROFLUOROMETER FOR KINETIC STUDIES JRNL TITL 2 ON PROTEIN CRYSTALS IN COMBINATION WITH X-RAY DIFFRACTION JRNL REF BIOPHYS.J. V. 91 981 2006 JRNL REFN ISSN 0006-3495 JRNL PMID 16698776 JRNL DOI 10.1529/BIOPHYSJ.105.078931 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 39138 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2055 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2871 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 146 REMARK 3 BIN FREE R VALUE : 0.3090 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 : 55 REMARK 3 SOLVENT ATOMS : 199 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.99000 REMARK 3 B22 (A**2) : -0.99000 REMARK 3 B33 (A**2) : 1.98000 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): 0.064 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.065 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.301 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2784 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2452 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3778 ; 1.753 ; 2.008 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5700 ; 0.832 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 330 ; 6.807 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;37.894 ;24.493 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 480 ;14.572 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;18.682 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 414 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3074 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 542 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 157 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1206 ; 0.192 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 645 ; 0.188 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 861 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 193 ; 0.240 ; 0.200 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): 15 ; 0.375 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 22 ; 0.373 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 30 ; 0.401 ; 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): 2154 ; 1.237 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2658 ; 1.306 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1363 ; 2.028 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1120 ; 2.808 ; 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 : 3 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 : X 1 X 169 REMARK 3 ORIGIN FOR THE GROUP (A): 19.0770 55.4100 -2.2640 REMARK 3 T TENSOR REMARK 3 T11: -0.0603 T22: -0.0625 REMARK 3 T33: -0.1319 T12: -0.0003 REMARK 3 T13: -0.0211 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 2.2879 L22: 2.2293 REMARK 3 L33: 0.8577 L12: -0.9779 REMARK 3 L13: -0.4125 L23: 0.2065 REMARK 3 S TENSOR REMARK 3 S11: 0.0557 S12: 0.1441 S13: 0.1094 REMARK 3 S21: -0.1510 S22: -0.0218 S23: -0.1128 REMARK 3 S31: -0.0259 S32: -0.0182 S33: -0.0339 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 : X 1167 X 1167 REMARK 3 ORIGIN FOR THE GROUP (A): 22.1380 67.4790 -0.7610 REMARK 3 T TENSOR REMARK 3 T11: -0.0739 T22: -0.0761 REMARK 3 T33: 0.0762 T12: 0.0142 REMARK 3 T13: -0.0166 T23: 0.0156 REMARK 3 L TENSOR REMARK 3 L11: 2.0927 L22: 4.2510 REMARK 3 L33: 17.1872 L12: 2.6013 REMARK 3 L13: 0.9802 L23: 1.5085 REMARK 3 S TENSOR REMARK 3 S11: 0.0067 S12: 0.1611 S13: 0.4985 REMARK 3 S21: -0.2216 S22: 0.3069 S23: -0.3956 REMARK 3 S31: -0.4673 S32: 0.2758 S33: -0.3135 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : X 2001 X 2321 REMARK 3 ORIGIN FOR THE GROUP (A): 19.6260 54.2520 0.9570 REMARK 3 T TENSOR REMARK 3 T11: 0.1136 T22: 0.0875 REMARK 3 T33: 0.0226 T12: -0.0215 REMARK 3 T13: -0.0389 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 3.2986 L22: 3.1585 REMARK 3 L33: 1.2443 L12: -1.2026 REMARK 3 L13: -0.3022 L23: 0.6195 REMARK 3 S TENSOR REMARK 3 S11: -0.0172 S12: -0.0428 S13: -0.0235 REMARK 3 S21: 0.0400 S22: 0.0800 S23: -0.1231 REMARK 3 S31: 0.0466 S32: 0.0342 S33: -0.0628 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. AN IANBD FLUOROPHORE WAS ATTACHED TO CYS-32. THE REMARK 3 STRUCTURE WAS REFINED USING TWO ALTERNATIVE CONFORMATIONS FOR REMARK 3 THE WHOLE PROTEIN CHAIN. THE CLOSE CONTACTS WITH WATER MOLECULES REMARK 3 ARE CAUSED BY THE TREATMENT OF THE WHOLE PROTEIN CHAIN WITH TWO REMARK 3 ALTERNATIVE CONFORMATIONS, BUT ONLY ONE POSITION PER WATER REMARK 3 MOLECULE. REMARK 4 REMARK 4 2CLC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-APR-06. REMARK 100 THE DEPOSITION ID IS D_1290028582. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.20 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41195 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 69.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.270 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.140 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: PDB ENTRY 5P21 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 13.35 MG/ML PROTEIN, REMARK 280 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM REMARK 280 SODIUM AZIDE; RESERVOIR SOLUTION: 100 MM HEPES PH 7.2, 200 MM REMARK 280 MAGNESIUM ACETATE, 16% PEG 8000 FRESHLY PREPARED) MIXTURE OF REMARK 280 EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291.15K, PH 7.20 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.50500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 8.75250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.25750 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 APPLY THE FOLLOWING TO CHAINS: X 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 400 REMARK 400 COMPOUND REMARK 400 RAS PROTEINS BIND GDP/GTP AND POSSESS INTRINSIC GTPASE REMARK 400 ACTIVITY REMARK 400 ENGINEERED RESIDUE IN CHAIN X, TYR 32 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN X, CYS 118 TO SER 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 1 CYS X 51 CB CYS X 51 SG 0.112 REMARK 500 1 GLN X 70 CD GLN X 70 OE1 0.171 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 1 PRO X 34 84.12 -65.23 REMARK 500 1 THR X 35 153.93 -43.05 REMARK 500 1 ILE X 36 -79.04 -109.17 REMARK 500 1 LYS X 117 36.99 77.32 REMARK 500 1 ARG X 149 -9.03 79.50 REMARK 500 2 GLU X 37 118.11 -178.47 REMARK 500 2 GLN X 61 115.64 133.23 REMARK 500 2 ASP X 107 -168.16 -72.46 REMARK 500 2 LYS X 117 35.98 73.95 REMARK 500 2 VAL X 152 -77.03 -56.07 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 X 106 ASP X 107 2 147.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH X2129 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH X2190 DISTANCE = 7.55 ANGSTROMS REMARK 525 HOH X2133 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH X2190 DISTANCE = 9.78 ANGSTROMS 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 X 168 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER X 17 OG REMARK 620 2 THR X 35 OG1 94.1 REMARK 620 3 GTP X1167 O1G 167.7 88.6 REMARK 620 4 GTP X1167 O1B 99.4 166.3 78.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 168 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 169 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XY2 X 332 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP X 1167 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CL0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H -RAS P21 IN REMARK 900 COMPLEX WITH GPPNHP REMARK 900 RELATED ID: 2CL6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H -RAS P21 IN REMARK 900 COMPLEX WITH S-CAGED GTP REMARK 900 RELATED ID: 2CL7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H -RAS P21 IN REMARK 900 COMPLEX WITH GTP REMARK 900 RELATED ID: 2CLD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H -RAS P21 IN REMARK 900 COMPLEX WITH GDP (2) DBREF 2CLC X 1 166 UNP P01112 RASH_HUMAN 1 166 SEQADV 2CLC CYS X 32 UNP P01112 TYR 32 ENGINEERED MUTATION SEQADV 2CLC SER X 118 UNP P01112 CYS 118 ENGINEERED MUTATION SEQRES 1 X 166 MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY GLY SEQRES 2 X 166 VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN ASN SEQRES 3 X 166 HIS PHE VAL ASP GLU CYS ASP PRO THR ILE GLU ASP SER SEQRES 4 X 166 TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS LEU SEQRES 5 X 166 LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SER SEQRES 6 X 166 ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY PHE SEQRES 7 X 166 LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE GLU SEQRES 8 X 166 ASP ILE HIS GLN TYR ARG GLU GLN ILE LYS ARG VAL LYS SEQRES 9 X 166 ASP SER ASP ASP VAL PRO MET VAL LEU VAL GLY ASN LYS SEQRES 10 X 166 SER ASP LEU ALA ALA ARG THR VAL GLU SER ARG GLN ALA SEQRES 11 X 166 GLN ASP LEU ALA ARG SER TYR GLY ILE PRO TYR ILE GLU SEQRES 12 X 166 THR SER ALA LYS THR ARG GLN GLY VAL GLU ASP ALA PHE SEQRES 13 X 166 TYR THR LEU VAL ARG GLU ILE ARG GLN HIS HET MG X 168 1 HET MG X 169 1 HET XY2 X 332 21 HET GTP X1167 32 HETNAM MG MAGNESIUM ION HETNAM XY2 N,N'-DIMETHYL-N-(ACETYL)-N'-(7-NITROBENZ-2-OXA-1,3- HETNAM 2 XY2 DIAZOL-4-YL)ETHYLENEDIAMINE HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 2 MG 2(MG 2+) FORMUL 4 XY2 C12 H15 N5 O4 FORMUL 5 GTP C10 H16 N5 O14 P3 FORMUL 6 HOH *199(H2 O) HELIX 1 1 GLY X 15 ASN X 26 1 12 HELIX 2 2 SER X 65 ARG X 73 1 9 HELIX 3 3 ASN X 86 ASP X 92 1 7 HELIX 4 4 ASP X 92 LYS X 104 1 13 HELIX 5 5 GLU X 126 GLY X 138 1 13 HELIX 6 6 GLY X 151 HIS X 166 1 16 SHEET 1 XA 6 GLU X 37 ILE X 46 0 SHEET 2 XA 6 GLU X 49 THR X 58 -1 O GLU X 49 N ILE X 46 SHEET 3 XA 6 THR X 2 VAL X 9 1 O THR X 2 N LEU X 52 SHEET 4 XA 6 GLY X 77 ALA X 83 1 O GLY X 77 N VAL X 7 SHEET 5 XA 6 MET X 111 ASN X 116 1 O VAL X 112 N CYS X 80 SHEET 6 XA 6 TYR X 141 THR X 144 1 O ILE X 142 N GLY X 115 LINK SG ACYS X 32 C19AXY2 X 332 1555 1555 1.77 LINK OG ASER X 17 MG A MG X 168 1555 1555 2.07 LINK OG1ATHR X 35 MG A MG X 168 1555 1555 2.03 LINK MG A MG X 168 O1GAGTP X1167 1555 1555 2.33 LINK MG A MG X 168 O1BAGTP X1167 1555 1555 2.14 SITE 1 AC1 5 SER X 17 THR X 35 GTP X1167 HOH X2170 SITE 2 AC1 5 HOH X2176 SITE 1 AC2 6 ASP X 108 HIS X 166 HOH X2026 HOH X2119 SITE 2 AC2 6 HOH X2171 HOH X2174 SITE 1 AC3 8 CYS X 32 TYR X 64 ASP X 69 GLN X 99 SITE 2 AC3 8 ARG X 102 VAL X 103 GLN X 131 HOH X2143 SITE 1 AC4 28 GLY X 12 GLY X 13 VAL X 14 GLY X 15 SITE 2 AC4 28 LYS X 16 SER X 17 ALA X 18 PHE X 28 SITE 3 AC4 28 VAL X 29 ASP X 30 THR X 35 GLY X 60 SITE 4 AC4 28 ASN X 116 LYS X 117 ASP X 119 LEU X 120 SITE 5 AC4 28 SER X 145 ALA X 146 MG X 168 HOH X2047 SITE 6 AC4 28 HOH X2062 HOH X2103 HOH X2138 HOH X2140 SITE 7 AC4 28 HOH X2170 HOH X2172 HOH X2176 HOH X2179 CRYST1 69.320 69.320 35.010 90.00 90.00 90.00 P 41 4 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 0.014426 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014426 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028563 0.00000 MODEL 1