PDB Short entry for 1XTQ HEADER SIGNALING PROTEIN 24-OCT-04 1XTQ TITLE STRUCTURE OF SMALL GTPASE HUMAN RHEB IN COMPLEX WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTP-BINDING PROTEIN RHEB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GTPASE DOMAIN; COMPND 5 SYNONYM: RAS HOMOLOG ENRICHED IN BRAIN; COMPND 6 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: RHEB; 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: PET22B(+) KEYWDS BETA SADDLE, P-LOOP, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.YU,J.DING REVDAT 5 25-OCT-23 1XTQ 1 REMARK SEQADV LINK REVDAT 4 11-OCT-17 1XTQ 1 REMARK REVDAT 3 24-FEB-09 1XTQ 1 VERSN REVDAT 2 03-MAY-05 1XTQ 1 JRNL REVDAT 1 08-MAR-05 1XTQ 0 JRNL AUTH Y.YU,S.LI,X.XU,Y.LI,K.GUAN,E.ARNOLD,J.DING JRNL TITL STRUCTURAL BASIS FOR THE UNIQUE BIOLOGICAL FUNCTION OF SMALL JRNL TITL 2 GTPASE RHEB JRNL REF J.BIOL.CHEM. V. 280 17093 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15728574 JRNL DOI 10.1074/JBC.M501253200 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 11436 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 SET) : 0.219 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 575 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2945 REMARK 3 BIN FREE R VALUE : 0.3842 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 85 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1344 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 164 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 6.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED WEIGHTED FULL MATRIX LEAST SQUARES REMARK 3 PROCEDURE. REMARK 4 REMARK 4 1XTQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030758. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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 : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : TRUNCATE REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11457 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 14.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.02900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.12200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRIES 1KAO, 1GUA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM DIHYDROGENPHOSPHATE, PEG REMARK 280 8000, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 22.24000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.28500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.13000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.28500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.24000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.13000 REMARK 290 SMTRY3 4 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 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 MET A 1 REMARK 465 PRO A 2 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS A 176 REMARK 465 HIS A 177 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 PHE A 70 119.72 -39.58 REMARK 500 VAL A 110 -8.35 -57.57 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 20 OG REMARK 620 2 GDP A 201 O3B 84.9 REMARK 620 3 HOH A 203 O 83.4 93.8 REMARK 620 4 HOH A 204 O 163.2 100.4 111.8 REMARK 620 5 HOH A 205 O 83.3 82.8 166.5 81.7 REMARK 620 6 HOH A 206 O 85.0 167.7 91.9 87.4 89.1 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 MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XTR RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH GPPNHP REMARK 900 RELATED ID: 1XTS RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH GTP DBREF 1XTQ A 1 169 UNP Q15382 RHEB_HUMAN 1 169 SEQADV 1XTQ LEU A 170 UNP Q15382 EXPRESSION TAG SEQADV 1XTQ GLU A 171 UNP Q15382 EXPRESSION TAG SEQADV 1XTQ HIS A 172 UNP Q15382 EXPRESSION TAG SEQADV 1XTQ HIS A 173 UNP Q15382 EXPRESSION TAG SEQADV 1XTQ HIS A 174 UNP Q15382 EXPRESSION TAG SEQADV 1XTQ HIS A 175 UNP Q15382 EXPRESSION TAG SEQADV 1XTQ HIS A 176 UNP Q15382 EXPRESSION TAG SEQADV 1XTQ HIS A 177 UNP Q15382 EXPRESSION TAG SEQRES 1 A 177 MET PRO GLN SER LYS SER ARG LYS ILE ALA ILE LEU GLY SEQRES 2 A 177 TYR ARG SER VAL GLY LYS SER SER LEU THR ILE GLN PHE SEQRES 3 A 177 VAL GLU GLY GLN PHE VAL ASP SER TYR ASP PRO THR ILE SEQRES 4 A 177 GLU ASN THR PHE THR LYS LEU ILE THR VAL ASN GLY GLN SEQRES 5 A 177 GLU TYR HIS LEU GLN LEU VAL ASP THR ALA GLY GLN ASP SEQRES 6 A 177 GLU TYR SER ILE PHE PRO GLN THR TYR SER ILE ASP ILE SEQRES 7 A 177 ASN GLY TYR ILE LEU VAL TYR SER VAL THR SER ILE LYS SEQRES 8 A 177 SER PHE GLU VAL ILE LYS VAL ILE HIS GLY LYS LEU LEU SEQRES 9 A 177 ASP MET VAL GLY LYS VAL GLN ILE PRO ILE MET LEU VAL SEQRES 10 A 177 GLY ASN LYS LYS ASP LEU HIS MET GLU ARG VAL ILE SER SEQRES 11 A 177 TYR GLU GLU GLY LYS ALA LEU ALA GLU SER TRP ASN ALA SEQRES 12 A 177 ALA PHE LEU GLU SER SER ALA LYS GLU ASN GLN THR ALA SEQRES 13 A 177 VAL ASP VAL PHE ARG ARG ILE ILE LEU GLU ALA GLU LYS SEQRES 14 A 177 LEU GLU HIS HIS HIS HIS HIS HIS HET MG A 202 1 HET GDP A 201 28 HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 GDP C10 H15 N5 O11 P2 FORMUL 4 HOH *164(H2 O) HELIX 1 1 GLY A 18 GLY A 29 1 12 HELIX 2 2 PRO A 71 SER A 75 5 5 HELIX 3 3 SER A 89 GLY A 108 1 20 HELIX 4 4 LEU A 123 ARG A 127 5 5 HELIX 5 5 SER A 130 ASN A 142 1 13 HELIX 6 6 GLU A 152 GLU A 171 1 20 SHEET 1 A 6 ASN A 41 VAL A 49 0 SHEET 2 A 6 GLN A 52 ASP A 60 -1 O LEU A 56 N LYS A 45 SHEET 3 A 6 LYS A 5 GLY A 13 1 N ILE A 9 O VAL A 59 SHEET 4 A 6 GLY A 80 SER A 86 1 O ILE A 82 N LEU A 12 SHEET 5 A 6 ILE A 114 ASN A 119 1 O VAL A 117 N LEU A 83 SHEET 6 A 6 ALA A 144 GLU A 147 1 O ALA A 144 N LEU A 116 LINK OG SER A 20 MG MG A 202 1555 1555 2.35 LINK O3B GDP A 201 MG MG A 202 1555 1555 2.42 LINK MG MG A 202 O HOH A 203 1555 1555 2.38 LINK MG MG A 202 O HOH A 204 1555 1555 2.36 LINK MG MG A 202 O HOH A 205 1555 1555 2.36 LINK MG MG A 202 O HOH A 206 1555 1555 2.42 SITE 1 AC1 6 SER A 20 GDP A 201 HOH A 203 HOH A 204 SITE 2 AC1 6 HOH A 205 HOH A 206 SITE 1 AC2 23 SER A 16 VAL A 17 GLY A 18 LYS A 19 SITE 2 AC2 23 SER A 20 SER A 21 PHE A 31 ASN A 119 SITE 3 AC2 23 LYS A 120 ASP A 122 LEU A 123 SER A 149 SITE 4 AC2 23 ALA A 150 LYS A 151 MG A 202 HOH A 203 SITE 5 AC2 23 HOH A 204 HOH A 208 HOH A 268 HOH A 325 SITE 6 AC2 23 HOH A 331 HOH A 343 HOH A 355 CRYST1 44.480 52.260 70.570 90.00 90.00 90.00 P 21 21 21 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 0.022482 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019135 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014170 0.00000