HEADER TRANSPORT PROTEIN 25-OCT-05 2ERX TITLE CRYSTAL STRUCTURE OF DIRAS2 IN COMPLEX WITH GDP AND INORGANIC TITLE 2 PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTP-BINDING PROTEIN DI-RAS2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DISTINCT SUBGROUP OF THE RAS FAMILY MEMBER 2; 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: DIRAS2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)R3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS DIRAS2, GTP HYDROLYSIS, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.PAPAGRIGORIOU,X.YANG,J.ELKINS,F.E.NIESEN,N.BURGESS,E.SALAH, AUTHOR 2 O.FEDOROV,L.J.BALL,F.VON DELFT,M.SUNDSTROM,A.EDWARDS,C.ARROWSMITH, AUTHOR 3 J.WEIGELT,D.DOYLE REVDAT 6 30-OCT-24 2ERX 1 REMARK REVDAT 5 23-AUG-23 2ERX 1 REMARK LINK REVDAT 4 24-FEB-09 2ERX 1 VERSN REVDAT 3 20-DEC-05 2ERX 1 AUTHOR REVDAT 2 15-NOV-05 2ERX 1 AUTHOR REVDAT 1 01-NOV-05 2ERX 0 JRNL AUTH E.PAPAGRIGORIOU,X.YANG,J.ELKINS,F.E.NIESEN,N.BURGESS, JRNL AUTH 2 E.SALAH,O.FEDOROV,L.J.BALL,F.VON DELFT,M.SUNDSTROM, JRNL AUTH 3 A.EDWARDS,C.ARROWSMITH,J.WEIGELT,D.DOYLE JRNL TITL CRYSTAL STRUCTURE OF DIRAS2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 40813 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2162 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2958 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.1710 REMARK 3 BIN FREE R VALUE SET COUNT : 140 REMARK 3 BIN FREE R VALUE : 0.2340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2539 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.95000 REMARK 3 B22 (A**2) : -1.50000 REMARK 3 B33 (A**2) : 2.45000 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): 0.083 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.599 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2650 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2432 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3593 ; 1.729 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5626 ; 1.168 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 329 ; 5.592 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;37.902 ;23.229 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 457 ;12.187 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ; 9.009 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 425 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2846 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 529 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 454 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2319 ; 0.197 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1312 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1488 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 148 ; 0.135 ; 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): 2 ; 0.215 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 36 ; 0.295 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.177 ; 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): 1778 ; 3.441 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 679 ; 0.826 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2677 ; 4.359 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1094 ; 6.081 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 916 ; 8.569 ;11.000 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 6 A 173 6 REMARK 3 1 B 5 B 173 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 A (A): 2355 ; 0.52 ; 5.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 2355 ; 2.10 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 REMARK 4 REMARK 4 2ERX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000035017. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98400 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42390 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 46.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.24140 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23200 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY: 1KAO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350; 0.20M SODIUM CHLORIDE; REMARK 280 0.1M BIS-TRIS, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 27.52050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.84550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.46550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.84550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.52050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.46550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 SER A 5 REMARK 465 ASP A 110 REMARK 465 VAL A 111 REMARK 465 GLU A 112 REMARK 465 ASP B 51 REMARK 465 LYS B 52 REMARK 465 GLY B 109 REMARK 465 ASP B 110 REMARK 465 VAL B 111 REMARK 465 GLU B 112 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 ASP A 51 CG OD1 OD2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 GLN A 67 CG CD OE1 NE2 REMARK 470 ARG A 91 CD NE CZ NH1 NH2 REMARK 470 GLN A 92 CD OE1 NE2 REMARK 470 GLU A 95 OE1 OE2 REMARK 470 LYS A 98 CD CE NZ REMARK 470 GLU A 102 CD OE1 OE2 REMARK 470 GLU A 135 CD OE1 OE2 REMARK 470 LYS A 144 CE NZ REMARK 470 LYS A 159 CE NZ REMARK 470 GLU A 164 CD OE1 OE2 REMARK 470 ASN A 167 CG OD1 ND2 REMARK 470 GLU B 34 CD OE1 OE2 REMARK 470 HIS B 66 CG ND1 CD2 CE1 NE2 REMARK 470 GLN B 67 CG CD OE1 NE2 REMARK 470 ARG B 73 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 95 CG CD OE1 OE2 REMARK 470 GLU B 102 CG CD OE1 OE2 REMARK 470 GLU B 106 CG CD OE1 OE2 REMARK 470 GLU B 130 CD OE1 OE2 REMARK 470 GLU B 137 CD OE1 OE2 REMARK 470 ARG B 141 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 144 CD CE NZ REMARK 470 LYS B 159 CD CE NZ REMARK 470 GLU B 164 CG CD OE1 OE2 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 OG SER A 35 OG SER B 133 4556 2.17 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 CYS A 55 CA - CB - SG ANGL. DEV. = 6.6 DEGREES REMARK 500 MET A 148 CG - SD - CE ANGL. DEV. = -11.5 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 VAL A 40 -64.93 -97.59 REMARK 500 ASP A 51 -130.94 52.52 REMARK 500 LYS A 52 49.86 -100.38 REMARK 500 LYS A 122 30.77 73.06 REMARK 500 VAL B 40 -63.30 -94.18 REMARK 500 LYS B 122 34.97 70.39 REMARK 500 GLU B 125 47.64 -89.45 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 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 21 OG REMARK 620 2 THR A 39 OG1 82.3 REMARK 620 3 GDP A 401 O3B 91.0 171.8 REMARK 620 4 PO4 A 402 O2 165.4 84.8 102.4 REMARK 620 5 HOH A 494 O 91.8 89.1 86.3 94.8 REMARK 620 6 HOH A 495 O 84.3 90.9 93.2 89.1 176.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 21 OG REMARK 620 2 THR B 39 OG1 82.0 REMARK 620 3 GDP B 401 O3B 90.3 170.9 REMARK 620 4 PO4 B 402 O4 166.6 86.5 101.7 REMARK 620 5 HOH B 477 O 85.6 89.3 94.8 87.6 REMARK 620 6 HOH B 483 O 89.6 88.8 86.4 96.9 175.1 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 PO4 B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 401 DBREF 2ERX A 5 176 UNP Q96HU8 DIRA2_HUMAN 5 176 DBREF 2ERX B 5 176 UNP Q96HU8 DIRA2_HUMAN 5 176 SEQRES 1 A 172 SER ASN ASP TYR ARG VAL ALA VAL PHE GLY ALA GLY GLY SEQRES 2 A 172 VAL GLY LYS SER SER LEU VAL LEU ARG PHE VAL LYS GLY SEQRES 3 A 172 THR PHE ARG GLU SER TYR ILE PRO THR VAL GLU ASP THR SEQRES 4 A 172 TYR ARG GLN VAL ILE SER CYS ASP LYS SER ILE CYS THR SEQRES 5 A 172 LEU GLN ILE THR ASP THR THR GLY SER HIS GLN PHE PRO SEQRES 6 A 172 ALA MET GLN ARG LEU SER ILE SER LYS GLY HIS ALA PHE SEQRES 7 A 172 ILE LEU VAL TYR SER ILE THR SER ARG GLN SER LEU GLU SEQRES 8 A 172 GLU LEU LYS PRO ILE TYR GLU GLN ILE CYS GLU ILE LYS SEQRES 9 A 172 GLY ASP VAL GLU SER ILE PRO ILE MET LEU VAL GLY ASN SEQRES 10 A 172 LYS CYS ASP GLU SER PRO SER ARG GLU VAL GLN SER SER SEQRES 11 A 172 GLU ALA GLU ALA LEU ALA ARG THR TRP LYS CYS ALA PHE SEQRES 12 A 172 MET GLU THR SER ALA LYS LEU ASN HIS ASN VAL LYS GLU SEQRES 13 A 172 LEU PHE GLN GLU LEU LEU ASN LEU GLU LYS ARG ARG THR SEQRES 14 A 172 VAL SER LEU SEQRES 1 B 172 SER ASN ASP TYR ARG VAL ALA VAL PHE GLY ALA GLY GLY SEQRES 2 B 172 VAL GLY LYS SER SER LEU VAL LEU ARG PHE VAL LYS GLY SEQRES 3 B 172 THR PHE ARG GLU SER TYR ILE PRO THR VAL GLU ASP THR SEQRES 4 B 172 TYR ARG GLN VAL ILE SER CYS ASP LYS SER ILE CYS THR SEQRES 5 B 172 LEU GLN ILE THR ASP THR THR GLY SER HIS GLN PHE PRO SEQRES 6 B 172 ALA MET GLN ARG LEU SER ILE SER LYS GLY HIS ALA PHE SEQRES 7 B 172 ILE LEU VAL TYR SER ILE THR SER ARG GLN SER LEU GLU SEQRES 8 B 172 GLU LEU LYS PRO ILE TYR GLU GLN ILE CYS GLU ILE LYS SEQRES 9 B 172 GLY ASP VAL GLU SER ILE PRO ILE MET LEU VAL GLY ASN SEQRES 10 B 172 LYS CYS ASP GLU SER PRO SER ARG GLU VAL GLN SER SER SEQRES 11 B 172 GLU ALA GLU ALA LEU ALA ARG THR TRP LYS CYS ALA PHE SEQRES 12 B 172 MET GLU THR SER ALA LYS LEU ASN HIS ASN VAL LYS GLU SEQRES 13 B 172 LEU PHE GLN GLU LEU LEU ASN LEU GLU LYS ARG ARG THR SEQRES 14 B 172 VAL SER LEU HET PO4 A 402 5 HET MG A 403 1 HET GDP A 401 28 HET PO4 B 402 5 HET MG B 403 1 HET GDP B 401 28 HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 3 PO4 2(O4 P 3-) FORMUL 4 MG 2(MG 2+) FORMUL 5 GDP 2(C10 H15 N5 O11 P2) FORMUL 9 HOH *205(H2 O) HELIX 1 1 GLY A 19 LYS A 29 1 11 HELIX 2 2 PHE A 68 GLY A 79 1 12 HELIX 3 3 SER A 90 GLU A 96 1 7 HELIX 4 4 LEU A 97 GLY A 109 1 13 HELIX 5 5 LYS A 122 ARG A 129 5 8 HELIX 6 6 GLN A 132 LYS A 144 1 13 HELIX 7 7 ASN A 157 LEU A 168 1 12 HELIX 8 8 GLY B 19 GLY B 30 1 12 HELIX 9 9 PHE B 68 GLY B 79 1 12 HELIX 10 10 SER B 90 GLU B 96 1 7 HELIX 11 11 GLU B 96 LYS B 108 1 13 HELIX 12 12 GLU B 125 ARG B 129 5 5 HELIX 13 13 GLN B 132 LYS B 144 1 13 HELIX 14 14 ASN B 157 GLU B 169 1 13 SHEET 1 A 7 ALA A 146 GLU A 149 0 SHEET 2 A 7 ILE A 116 ASN A 121 1 N LEU A 118 O ALA A 146 SHEET 3 A 7 ALA A 81 SER A 87 1 N TYR A 86 O ASN A 121 SHEET 4 A 7 ASP A 7 PHE A 13 1 N PHE A 13 O VAL A 85 SHEET 5 A 7 SER A 53 ASP A 61 1 O GLN A 58 N VAL A 10 SHEET 6 A 7 ASP A 42 CYS A 50 -1 N TYR A 44 O ILE A 59 SHEET 7 A 7 VAL A 174 SER A 175 -1 O SER A 175 N SER A 49 SHEET 1 B12 ALA A 146 GLU A 149 0 SHEET 2 B12 ILE A 116 ASN A 121 1 N LEU A 118 O ALA A 146 SHEET 3 B12 ALA A 81 SER A 87 1 N TYR A 86 O ASN A 121 SHEET 4 B12 ASP A 7 PHE A 13 1 N PHE A 13 O VAL A 85 SHEET 5 B12 SER A 53 ASP A 61 1 O GLN A 58 N VAL A 10 SHEET 6 B12 ASP A 42 CYS A 50 -1 N TYR A 44 O ILE A 59 SHEET 7 B12 ASP B 42 ILE B 48 -1 O THR B 43 N THR A 43 SHEET 8 B12 CYS B 55 ASP B 61 -1 O ASP B 61 N ASP B 42 SHEET 9 B12 TYR B 8 PHE B 13 1 N TYR B 8 O GLN B 58 SHEET 10 B12 ALA B 81 SER B 87 1 O ILE B 83 N PHE B 13 SHEET 11 B12 ILE B 116 ASN B 121 1 O ASN B 121 N TYR B 86 SHEET 12 B12 ALA B 146 GLU B 149 1 O ALA B 146 N LEU B 118 SSBOND 1 CYS B 50 CYS B 55 1555 1555 2.00 LINK OG SER A 21 MG MG A 403 1555 1555 2.12 LINK OG1 THR A 39 MG MG A 403 1555 1555 2.11 LINK O3B GDP A 401 MG MG A 403 1555 1555 2.06 LINK O2 PO4 A 402 MG MG A 403 1555 1555 2.03 LINK MG MG A 403 O HOH A 494 1555 1555 2.04 LINK MG MG A 403 O HOH A 495 1555 1555 2.09 LINK OG SER B 21 MG MG B 403 1555 1555 2.07 LINK OG1 THR B 39 MG MG B 403 1555 1555 2.11 LINK O3B GDP B 401 MG MG B 403 1555 1555 2.07 LINK O4 PO4 B 402 MG MG B 403 1555 1555 2.02 LINK MG MG B 403 O HOH B 477 1555 1555 2.03 LINK MG MG B 403 O HOH B 483 1555 1555 2.09 SITE 1 AC1 11 GLY B 16 LYS B 20 TYR B 36 THR B 39 SITE 2 AC1 11 THR B 63 GLY B 64 SER B 65 GDP B 401 SITE 3 AC1 11 MG B 403 HOH B 477 HOH B 483 SITE 1 AC2 6 SER B 21 THR B 39 GDP B 401 PO4 B 402 SITE 2 AC2 6 HOH B 477 HOH B 483 SITE 1 AC3 10 GLY A 16 LYS A 20 TYR A 36 THR A 39 SITE 2 AC3 10 THR A 63 GLY A 64 GDP A 401 MG A 403 SITE 3 AC3 10 HOH A 494 HOH A 495 SITE 1 AC4 6 SER A 21 THR A 39 GDP A 401 PO4 A 402 SITE 2 AC4 6 HOH A 494 HOH A 495 SITE 1 AC5 25 GLY B 17 VAL B 18 GLY B 19 LYS B 20 SITE 2 AC5 25 SER B 21 SER B 22 PHE B 32 ARG B 33 SITE 3 AC5 25 GLU B 34 TYR B 36 ASN B 121 LYS B 122 SITE 4 AC5 25 ASP B 124 GLU B 125 SER B 151 ALA B 152 SITE 5 AC5 25 LYS B 153 PO4 B 402 MG B 403 HOH B 407 SITE 6 AC5 25 HOH B 414 HOH B 440 HOH B 477 HOH B 483 SITE 7 AC5 25 HOH B 492 SITE 1 AC6 24 GLY A 17 VAL A 18 GLY A 19 LYS A 20 SITE 2 AC6 24 SER A 21 SER A 22 PHE A 32 ARG A 33 SITE 3 AC6 24 GLU A 34 TYR A 36 ASN A 121 LYS A 122 SITE 4 AC6 24 ASP A 124 GLU A 125 SER A 151 ALA A 152 SITE 5 AC6 24 LYS A 153 PO4 A 402 MG A 403 HOH A 445 SITE 6 AC6 24 HOH A 464 HOH A 486 HOH A 494 HOH A 495 CRYST1 55.041 74.931 85.691 90.00 90.00 90.00 P 21 21 21 8 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 0.018168 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011670 0.00000