HEADER PROTEIN BINDING 07-MAY-13 4KLZ TITLE INHIBITION OF SMALL GTPASES BY STABILIZATION OF THE GDP COMPLEX, A TITLE 2 NOVEL APPROACH APPLIED TO RIT1, A TARGET FOR RHEUMATOID ARTHRITIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTP-BINDING PROTEIN RIT1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GTP BINDING DOMAIN, UNP RESIDUES 19-189; COMPND 5 SYNONYM: RAS-LIKE PROTEIN EXPRESSED IN MANY TISSUES, RAS-LIKE WITHOUT COMPND 6 CAAX PROTEIN 1; COMPND 7 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: RIT1, RIBB, RIT, ROC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3+ RP; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQTEV KEYWDS SMALL GTPASE, MOLECULAR SWITCH (GTPASE), GDP/GTP BINDING, PROTEIN KEYWDS 2 BINDING, GUANINE NUCLEOTIDE BINDING EXPDTA X-RAY DIFFRACTION AUTHOR D.M.SHAH,M.KOBAYASHI,P.H.KEIZERS,A.W.TUIN,E.AB,L.MANNING, AUTHOR 2 A.A.RZEPIELA,M.ANDREWS,F.J.HOEDEMAEKER,G.SIEGAL REVDAT 2 20-SEP-23 4KLZ 1 REMARK SEQADV LINK REVDAT 1 17-SEP-14 4KLZ 0 JRNL AUTH D.M.SHAH,M.KOBAYASHI,P.H.KEIZERS,A.W.TUIN,E.AB,L.MANNING, JRNL AUTH 2 A.A.RZEPIELA,M.ANDREWS,F.J.HOEDEMAEKER,G.SIEGAL JRNL TITL INHIBITION OF SMALL GTPASES BY STABILIZATION OF THE GDP JRNL TITL 2 COMPLEX, A NOVEL APPROACH APPLIED TO RIT1, A TARGET FOR JRNL TITL 3 RHEUMATOID ARTHRITIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 4860 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.311 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 520 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 335 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.1740 REMARK 3 BIN FREE R VALUE SET COUNT : 47 REMARK 3 BIN FREE R VALUE : 0.4170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1278 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.07000 REMARK 3 B22 (A**2) : -1.11000 REMARK 3 B33 (A**2) : -0.99000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.390 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.285 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.230 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.833 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1345 ; 0.042 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 951 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1817 ; 3.177 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2283 ; 1.567 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 158 ;12.193 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 70 ;37.123 ;22.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 240 ;23.608 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;21.704 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 194 ; 0.181 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1474 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 306 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 368 ; 0.307 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1041 ; 0.270 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 595 ; 0.221 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 750 ; 0.108 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 50 ; 0.270 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.012 ; 0.200 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): 32 ; 0.251 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 96 ; 0.360 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.446 ; 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): 975 ; 1.678 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 317 ; 0.368 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1261 ; 2.063 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 661 ; 3.337 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 554 ; 4.403 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4KLZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079505. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 99 REMARK 200 PH : 7.0-7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54146 REMARK 200 MONOCHROMATOR : CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS PLUS REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5464 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05470 REMARK 200 FOR THE DATA SET : 36.4500 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: COOT REMARK 200 STARTING MODEL: PDB ENTRY 2ERY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 11-14% W/V PEG4000, 5-8% V/V JEFFAMINE REMARK 280 M600, IMIDAZOLE , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 18.52400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 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 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 17 REMARK 465 SER A 18 REMARK 465 SER A 19 REMARK 465 ARG A 20 REMARK 465 GLN A 79 REMARK 465 ALA A 80 REMARK 465 GLU A 81 REMARK 465 PHE A 82 REMARK 465 THR A 83 REMARK 465 ALA A 84 REMARK 465 MET A 85 REMARK 465 ARG A 86 REMARK 465 ASP A 87 REMARK 465 GLU A 186 REMARK 465 LYS A 187 REMARK 465 GLU A 188 REMARK 465 ALA A 189 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 ASP A 66 N PRO A 68 1.97 REMARK 500 NZ LYS A 23 O ALA A 92 2.08 REMARK 500 OH TYR A 169 O HOH A 616 2.16 REMARK 500 O GLU A 48 O2' GDP A 501 2.16 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 GLY A 78 OH TYR A 167 2655 1.88 REMARK 500 NH2 ARG A 45 OD1 ASP A 104 2645 2.13 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 GLU A 48 CG GLU A 48 CD 0.099 REMARK 500 VAL A 130 CB VAL A 130 CG1 -0.140 REMARK 500 VAL A 132 CB VAL A 132 CG2 0.142 REMARK 500 ARG A 142 CG ARG A 142 CD 0.259 REMARK 500 CYS A 158 CB CYS A 158 SG -0.389 REMARK 500 TYR A 169 CE1 TYR A 169 CZ -0.088 REMARK 500 TYR A 170 CZ TYR A 170 CE2 -0.087 REMARK 500 GLU A 181 CG GLU A 181 CD -0.103 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 MET A 26 CG - SD - CE ANGL. DEV. = 10.0 DEGREES REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 72 CB - CG - OD1 ANGL. DEV. = 11.6 DEGREES REMARK 500 ASP A 72 CB - CG - OD2 ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 106 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 122 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 122 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 LEU A 141 CA - CB - CG ANGL. DEV. = 17.4 DEGREES REMARK 500 ARG A 142 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 142 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 154 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 ARG A 154 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 CYS A 158 N - CA - CB ANGL. DEV. = -12.5 DEGREES REMARK 500 GLU A 181 OE1 - CD - OE2 ANGL. DEV. = 8.0 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 SER A 43 24.32 -145.91 REMARK 500 ASP A 65 -42.34 31.45 REMARK 500 ASP A 66 -58.51 -171.35 REMARK 500 GLU A 67 55.74 2.71 REMARK 500 ALA A 77 65.85 -100.08 REMARK 500 TYR A 89 17.21 -61.69 REMARK 500 VAL A 121 -78.55 -96.83 REMARK 500 ARG A 123 64.26 90.65 REMARK 500 THR A 124 -164.31 -161.40 REMARK 500 ASP A 126 44.65 -151.89 REMARK 500 LYS A 135 33.70 74.10 REMARK 500 SER A 157 89.96 35.13 REMARK 500 ARG A 168 56.87 35.60 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 ASP A 65 ASP A 66 135.93 REMARK 500 ALA A 77 GLY A 78 146.78 REMARK 500 PHE A 96 ILE A 97 147.77 REMARK 500 PHE A 156 SER A 157 -149.70 REMARK 500 SER A 157 CYS A 158 -144.37 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 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 35 OG REMARK 620 2 GDP A 501 O2B 93.8 REMARK 620 3 HOH A 618 O 67.8 86.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5P21 RELATED DB: PDB REMARK 900 REFINED CRYSTAL STRUCTURE OF THE TRIPHOSPHATE CONFORMATION OF H-RAS REMARK 900 P21 AT 1.35 ANGSTROMS RESOLUTION: IMPLICATIONS FOR THE MECHANISM OF REMARK 900 GTP HYDROLYSIS DBREF 4KLZ A 19 189 UNP Q92963 RIT1_HUMAN 19 189 SEQADV 4KLZ GLY A 17 UNP Q92963 EXPRESSION TAG SEQADV 4KLZ SER A 18 UNP Q92963 EXPRESSION TAG SEQRES 1 A 173 GLY SER SER ARG GLU TYR LYS LEU VAL MET LEU GLY ALA SEQRES 2 A 173 GLY GLY VAL GLY LYS SER ALA MET THR MET GLN PHE ILE SEQRES 3 A 173 SER HIS ARG PHE PRO GLU ASP HIS ASP PRO THR ILE GLU SEQRES 4 A 173 ASP ALA TYR LYS ILE ARG ILE ARG ILE ASP ASP GLU PRO SEQRES 5 A 173 ALA ASN LEU ASP ILE LEU ASP THR ALA GLY GLN ALA GLU SEQRES 6 A 173 PHE THR ALA MET ARG ASP GLN TYR MET ARG ALA GLY GLU SEQRES 7 A 173 GLY PHE ILE ILE CYS TYR SER ILE THR ASP ARG ARG SER SEQRES 8 A 173 PHE HIS GLU VAL ARG GLU PHE LYS GLN LEU ILE TYR ARG SEQRES 9 A 173 VAL ARG ARG THR ASP ASP THR PRO VAL VAL LEU VAL GLY SEQRES 10 A 173 ASN LYS SER ASP LEU LYS GLN LEU ARG GLN VAL THR LYS SEQRES 11 A 173 GLU GLU GLY LEU ALA LEU ALA ARG GLU PHE SER CYS PRO SEQRES 12 A 173 PHE PHE GLU THR SER ALA ALA TYR ARG TYR TYR ILE ASP SEQRES 13 A 173 ASP VAL PHE HIS ALA LEU VAL ARG GLU ILE ARG ARG LYS SEQRES 14 A 173 GLU LYS GLU ALA HET GDP A 501 28 HET MG A 502 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 HOH *18(H2 O) HELIX 1 1 GLY A 33 HIS A 44 1 12 HELIX 2 2 ASP A 104 GLU A 110 1 7 HELIX 3 3 GLU A 110 ARG A 122 1 13 HELIX 4 4 LEU A 138 ARG A 142 5 5 HELIX 5 5 THR A 145 PHE A 156 1 12 HELIX 6 6 SER A 164 ARG A 168 5 5 HELIX 7 7 TYR A 170 ARG A 183 1 14 SHEET 1 A 6 ASP A 56 ILE A 62 0 SHEET 2 A 6 ALA A 69 ASP A 75 -1 O ALA A 69 N ILE A 62 SHEET 3 A 6 TYR A 22 LEU A 27 1 N TYR A 22 O ASN A 70 SHEET 4 A 6 GLY A 95 SER A 101 1 O GLY A 95 N VAL A 25 SHEET 5 A 6 VAL A 129 ASN A 134 1 O ASN A 134 N TYR A 100 SHEET 6 A 6 PHE A 160 GLU A 162 1 O PHE A 161 N GLY A 133 LINK OG SER A 35 MG MG A 502 1555 1555 2.43 LINK O2B GDP A 501 MG MG A 502 1555 1555 1.99 LINK MG MG A 502 O HOH A 618 1555 1555 2.21 SITE 1 AC1 17 GLY A 31 VAL A 32 GLY A 33 LYS A 34 SITE 2 AC1 17 SER A 35 ALA A 36 PHE A 46 GLU A 48 SITE 3 AC1 17 ASN A 134 LYS A 135 ASP A 137 LEU A 138 SITE 4 AC1 17 SER A 164 ALA A 165 ALA A 166 MG A 502 SITE 5 AC1 17 HOH A 618 SITE 1 AC2 3 SER A 35 GDP A 501 HOH A 618 CRYST1 40.278 37.048 40.736 90.00 95.90 90.00 P 1 21 1 2 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 0.024827 0.000000 0.002565 0.00000 SCALE2 0.000000 0.026992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024679 0.00000