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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
