HEADER TRANSLATION 16-JAN-06 2DCU TITLE CRYSTAL STRUCTURE OF TRANSLATION INITIATION FACTOR AIF2BETAGAMMA TITLE 2 HETERODIMER WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSLATION INITIATION FACTOR 2 GAMMA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EIF-2-GAMMA, AIF2-GAMMA; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: EIF-2-BETA, AIF2-BETA; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 186497; SOURCE 4 STRAIN: DSM 3638; SOURCE 5 GENE: PF1717; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-CODONPLUS-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-26B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 13 ORGANISM_TAXID: 186497; SOURCE 14 STRAIN: DSM 3638; SOURCE 15 GENE: PF0481; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-CODONPLUS-RIL; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET-26B KEYWDS PROTEIN COMPLEX, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR M.SOKABE,M.YAO,N.SAKAI,S.TOYA,I.TANAKA REVDAT 7 25-OCT-23 2DCU 1 REMARK REVDAT 6 10-NOV-21 2DCU 1 REMARK SEQADV LINK REVDAT 5 13-JUL-11 2DCU 1 VERSN REVDAT 4 21-JUL-09 2DCU 1 JRNL REVDAT 3 24-FEB-09 2DCU 1 VERSN REVDAT 2 01-AUG-06 2DCU 1 TITLE REVDAT 1 25-JUL-06 2DCU 0 JRNL AUTH M.SOKABE,M.YAO,N.SAKAI,S.TOYA,I.TANAKA JRNL TITL STRUCTURE OF ARCHAEAL TRANSLATIONAL INITIATION FACTOR 2 JRNL TITL 2 BETAGAMMA-GDP REVEALS SIGNIFICANT CONFORMATIONAL CHANGE OF JRNL TITL 3 THE BETA-SUBUNIT AND SWITCH 1 REGION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 13016 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16924118 JRNL DOI 10.1073/PNAS.0604165103 REMARK 2 REMARK 2 RESOLUTION. 3.40 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) : 3.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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 : 6862 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) : 0.249 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 560 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.52 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 54 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 : 4250 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.70 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) : 0.44 REMARK 3 ESD FROM SIGMAA (A) : 0.57 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.55 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.83 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.063 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTOROPIC 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: NULL REMARK 4 REMARK 4 2DCU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000025263. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9788 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8036 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11900 REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49700 REMARK 200 FOR SHELL : 1.400 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 ENTRY 2D74 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8000, 0.1M TRIS-HCL, 0.2M REMARK 280 MAGNESIUM CHLORIDE, PH 8.5, 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 34.59900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.92850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.28050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.92850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.59900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.28050 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 GLU A 3 REMARK 465 LYS A 4 REMARK 465 ARG A 5 REMARK 465 GLU A 413 REMARK 465 HIS A 414 REMARK 465 HIS A 415 REMARK 465 HIS A 416 REMARK 465 HIS A 417 REMARK 465 HIS A 418 REMARK 465 HIS A 419 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 LEU B 140 REMARK 465 LEU B 141 REMARK 465 GLU B 142 REMARK 465 HIS B 143 REMARK 465 HIS B 144 REMARK 465 HIS B 145 REMARK 465 HIS B 146 REMARK 465 HIS B 147 REMARK 465 HIS B 148 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 NE ARG A 44 O HOH A 3044 2.09 REMARK 500 O LYS A 222 N GLY A 224 2.14 REMARK 500 O ALA B 15 CD2 LEU B 19 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 GLU A 41 N - CA - C ANGL. DEV. = -18.6 DEGREES REMARK 500 GLU A 42 N - CA - C ANGL. DEV. = 23.1 DEGREES REMARK 500 GLY A 46 N - CA - C ANGL. DEV. = 27.9 DEGREES REMARK 500 ILE A 49 N - CA - C ANGL. DEV. = -18.3 DEGREES REMARK 500 GLY A 224 N - CA - C ANGL. DEV. = -15.3 DEGREES REMARK 500 HIS A 261 N - CA - C ANGL. DEV. = -19.3 DEGREES REMARK 500 GLY A 262 N - CA - C ANGL. DEV. = -17.3 DEGREES REMARK 500 PRO B 20 C - N - CA ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG B 29 N - CA - C ANGL. DEV. = -23.8 DEGREES REMARK 500 LYS B 127 N - CA - C ANGL. DEV. = 17.7 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 HIS A 19 172.11 -59.29 REMARK 500 ASP A 21 -4.40 -151.10 REMARK 500 VAL A 34 11.14 -69.17 REMARK 500 HIS A 39 35.91 72.77 REMARK 500 SER A 40 95.98 -169.62 REMARK 500 GLU A 42 -24.86 -32.78 REMARK 500 ILE A 47 -114.92 -85.69 REMARK 500 LYS A 50 25.62 -57.02 REMARK 500 CYS A 73 118.38 -39.04 REMARK 500 TYR A 75 -75.44 -91.61 REMARK 500 SER A 91 113.39 -161.16 REMARK 500 CYS A 121 -72.61 -45.66 REMARK 500 ASN A 140 86.36 -69.54 REMARK 500 ASN A 187 13.88 86.93 REMARK 500 VAL A 220 -8.02 -56.70 REMARK 500 PRO A 223 72.35 -52.38 REMARK 500 THR A 225 -19.26 80.74 REMARK 500 GLU A 228 -125.81 -53.77 REMARK 500 LYS A 229 45.18 -90.62 REMARK 500 VAL A 231 148.04 -30.70 REMARK 500 ARG A 253 -100.53 -82.79 REMARK 500 GLU A 260 97.97 -25.23 REMARK 500 ARG A 263 -69.26 -104.58 REMARK 500 ALA A 278 113.79 -164.19 REMARK 500 LYS A 304 153.22 -49.02 REMARK 500 GLN A 341 -72.51 -56.04 REMARK 500 LEU A 343 -82.84 -53.53 REMARK 500 ASN A 344 87.24 -61.24 REMARK 500 LYS A 351 -3.02 86.12 REMARK 500 GLN A 396 -78.69 -65.79 REMARK 500 ILE A 397 84.81 70.81 REMARK 500 PRO B 20 176.22 -37.57 REMARK 500 GLU B 21 -71.67 -82.54 REMARK 500 ASN B 22 -33.64 -31.67 REMARK 500 HIS B 26 -75.20 -22.79 REMARK 500 LEU B 68 -13.82 -46.66 REMARK 500 ALA B 72 65.17 -119.44 REMARK 500 GLU B 78 146.12 -170.72 REMARK 500 TYR B 104 -5.86 -147.57 REMARK 500 ASP B 121 -177.78 -172.30 REMARK 500 LYS B 127 167.94 153.34 REMARK 500 CYS B 128 118.20 1.02 REMARK 500 GLU B 134 74.40 -115.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 16 0.07 SIDE CHAIN 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 A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 25 OG1 REMARK 620 2 GDP A2001 O3B 65.1 REMARK 620 3 HOH A3057 O 68.3 83.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A3001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 61 SG REMARK 620 2 CYS A 64 SG 100.5 REMARK 620 3 CYS A 73 SG 94.1 112.5 REMARK 620 4 CYS A 76 SG 93.4 145.4 97.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B3002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 107 SG REMARK 620 2 CYS B 110 SG 117.3 REMARK 620 3 CYS B 128 SG 122.2 115.8 REMARK 620 4 CYS B 131 SG 111.2 87.6 92.0 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 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 3002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D74 RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN APO FORM DBREF 2DCU A 1 411 UNP Q8U082 IF2G_PYRFU 1 411 DBREF 2DCU B 1 140 UNP Q8U3I5 IF2B_PYRFU 1 140 SEQADV 2DCU ASP A 236 UNP Q8U082 GLY 236 ENGINEERED MUTATION SEQADV 2DCU LEU A 412 UNP Q8U082 EXPRESSION TAG SEQADV 2DCU GLU A 413 UNP Q8U082 EXPRESSION TAG SEQADV 2DCU HIS A 414 UNP Q8U082 EXPRESSION TAG SEQADV 2DCU HIS A 415 UNP Q8U082 EXPRESSION TAG SEQADV 2DCU HIS A 416 UNP Q8U082 EXPRESSION TAG SEQADV 2DCU HIS A 417 UNP Q8U082 EXPRESSION TAG SEQADV 2DCU HIS A 418 UNP Q8U082 EXPRESSION TAG SEQADV 2DCU HIS A 419 UNP Q8U082 EXPRESSION TAG SEQADV 2DCU LEU B 141 UNP Q8U3I5 EXPRESSION TAG SEQADV 2DCU GLU B 142 UNP Q8U3I5 EXPRESSION TAG SEQADV 2DCU HIS B 143 UNP Q8U3I5 EXPRESSION TAG SEQADV 2DCU HIS B 144 UNP Q8U3I5 EXPRESSION TAG SEQADV 2DCU HIS B 145 UNP Q8U3I5 EXPRESSION TAG SEQADV 2DCU HIS B 146 UNP Q8U3I5 EXPRESSION TAG SEQADV 2DCU HIS B 147 UNP Q8U3I5 EXPRESSION TAG SEQADV 2DCU HIS B 148 UNP Q8U3I5 EXPRESSION TAG SEQRES 1 A 419 MET GLY GLU LYS ARG LYS THR ARG GLN ALA GLU VAL ASN SEQRES 2 A 419 ILE GLY MET VAL GLY HIS VAL ASP HIS GLY LYS THR THR SEQRES 3 A 419 LEU THR LYS ALA LEU THR GLY VAL TRP THR ASP THR HIS SEQRES 4 A 419 SER GLU GLU LEU ARG ARG GLY ILE THR ILE LYS ILE GLY SEQRES 5 A 419 PHE ALA ASP ALA GLU ILE ARG ARG CYS SER ASN CYS GLY SEQRES 6 A 419 ARG TYR SER THR SER PRO ILE CYS PRO TYR CYS GLY HIS SEQRES 7 A 419 GLU THR GLU PHE ILE ARG ARG VAL SER PHE ILE ASP SER SEQRES 8 A 419 PRO GLY HIS GLU ALA LEU MET THR THR MET LEU ALA GLY SEQRES 9 A 419 ALA SER LEU MET ASP GLY ALA ILE LEU VAL ILE ALA ALA SEQRES 10 A 419 ASN GLU PRO CYS PRO ARG PRO GLN THR ARG GLU HIS LEU SEQRES 11 A 419 MET ALA LEU GLN ILE ILE GLY GLN LYS ASN ILE ILE ILE SEQRES 12 A 419 ALA GLN ASN LYS ILE GLU LEU VAL ASP LYS GLU LYS ALA SEQRES 13 A 419 LEU GLU ASN TYR ARG GLN ILE LYS GLU PHE ILE LYS GLY SEQRES 14 A 419 THR VAL ALA GLU ASN ALA PRO ILE ILE PRO ILE SER ALA SEQRES 15 A 419 LEU HIS GLY ALA ASN ILE ASP VAL LEU VAL LYS ALA ILE SEQRES 16 A 419 GLU GLU PHE ILE PRO THR PRO LYS ARG ASP SER ASN LYS SEQRES 17 A 419 PRO PRO LYS MET LEU VAL LEU ARG SER PHE ASP VAL ASN SEQRES 18 A 419 LYS PRO GLY THR PRO PRO GLU LYS LEU VAL GLY GLY VAL SEQRES 19 A 419 LEU ASP GLY SER ILE VAL GLN GLY LYS LEU LYS VAL GLY SEQRES 20 A 419 ASP GLU ILE GLU ILE ARG PRO GLY VAL PRO TYR GLU GLU SEQRES 21 A 419 HIS GLY ARG ILE LYS TYR GLU PRO ILE THR THR GLU ILE SEQRES 22 A 419 VAL SER LEU GLN ALA GLY GLY GLN PHE VAL GLU GLU ALA SEQRES 23 A 419 TYR PRO GLY GLY LEU VAL GLY ILE GLY THR LYS LEU ASP SEQRES 24 A 419 PRO TYR LEU THR LYS GLY ASP LEU MET ALA GLY ASN VAL SEQRES 25 A 419 VAL GLY LYS PRO GLY LYS LEU PRO PRO VAL TRP THR ASP SEQRES 26 A 419 LEU ARG LEU GLU VAL HIS LEU LEU GLU ARG VAL VAL GLY SEQRES 27 A 419 THR GLU GLN GLU LEU ASN VAL GLU PRO ILE LYS ARG LYS SEQRES 28 A 419 GLU VAL LEU LEU LEU ASN VAL GLY THR ALA ARG THR MET SEQRES 29 A 419 GLY LEU VAL THR ALA LEU GLY LYS ASP GLU ILE GLU LEU SEQRES 30 A 419 LYS LEU GLN ILE PRO VAL CYS ALA GLU PRO GLY GLU ARG SEQRES 31 A 419 VAL ALA ILE SER ARG GLN ILE GLY SER ARG TRP ARG LEU SEQRES 32 A 419 ILE GLY TYR GLY ILE ILE LYS GLU LEU GLU HIS HIS HIS SEQRES 33 A 419 HIS HIS HIS SEQRES 1 B 148 MET GLU ILE ASP TYR TYR ASP TYR GLU LYS LEU LEU GLU SEQRES 2 B 148 LYS ALA TYR GLN GLU LEU PRO GLU ASN VAL LYS HIS HIS SEQRES 3 B 148 LYS SER ARG PHE GLU VAL PRO GLY ALA LEU VAL THR ILE SEQRES 4 B 148 GLU GLY ASN LYS THR ILE ILE GLU ASN PHE LYS ASP ILE SEQRES 5 B 148 ALA ASP ALA LEU ASN ARG ASP PRO GLN HIS LEU LEU LYS SEQRES 6 B 148 PHE LEU LEU ARG GLU ILE ALA THR ALA GLY THR LEU GLU SEQRES 7 B 148 GLY ARG ARG VAL VAL LEU GLN GLY ARG PHE THR PRO TYR SEQRES 8 B 148 LEU ILE ALA ASN LYS LEU LYS LYS TYR ILE LYS GLU TYR SEQRES 9 B 148 VAL ILE CYS PRO VAL CYS GLY SER PRO ASP THR LYS ILE SEQRES 10 B 148 ILE LYS ARG ASP ARG PHE HIS PHE LEU LYS CYS GLU ALA SEQRES 11 B 148 CYS GLY ALA GLU THR PRO ILE GLN HIS LEU LEU GLU HIS SEQRES 12 B 148 HIS HIS HIS HIS HIS HET MG A1001 1 HET ZN A3001 1 HET GDP A2001 28 HET ZN B3002 1 HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 3 MG MG 2+ FORMUL 4 ZN 2(ZN 2+) FORMUL 5 GDP C10 H15 N5 O11 P2 FORMUL 7 HOH *108(H2 O) HELIX 1 1 GLY A 23 GLY A 33 1 11 HELIX 2 2 VAL A 34 THR A 36 5 3 HELIX 3 3 GLY A 93 GLY A 104 1 12 HELIX 4 4 ARG A 123 ILE A 136 1 14 HELIX 5 5 LYS A 147 VAL A 151 5 5 HELIX 6 6 ASP A 152 LYS A 168 1 17 HELIX 7 7 ASN A 187 PHE A 198 1 12 HELIX 8 8 ASP A 299 LEU A 307 5 9 HELIX 9 9 THR A 339 ASN A 344 1 6 HELIX 10 10 ASP B 7 GLU B 18 1 12 HELIX 11 11 PRO B 20 HIS B 25 1 6 HELIX 12 12 ASN B 48 ASN B 57 1 10 HELIX 13 13 PRO B 60 ILE B 71 1 12 HELIX 14 14 THR B 89 VAL B 105 1 17 SHEET 1 A 7 TYR A 67 SER A 68 0 SHEET 2 A 7 GLY A 52 CYS A 61 -1 N ARG A 59 O SER A 68 SHEET 3 A 7 THR A 80 ASP A 90 -1 O PHE A 88 N ALA A 54 SHEET 4 A 7 ASN A 13 GLY A 18 1 N ILE A 14 O SER A 87 SHEET 5 A 7 GLY A 110 ALA A 116 1 O ILE A 112 N GLY A 15 SHEET 6 A 7 ILE A 141 ASN A 146 1 O ALA A 144 N LEU A 113 SHEET 7 A 7 ILE A 177 PRO A 179 1 O ILE A 178 N ILE A 143 SHEET 1 B 7 LYS A 211 PHE A 218 0 SHEET 2 B 7 VAL A 234 GLN A 241 -1 O ASP A 236 N ARG A 216 SHEET 3 B 7 VAL A 292 THR A 296 -1 O ILE A 294 N LEU A 235 SHEET 4 B 7 THR A 270 GLN A 277 -1 N VAL A 274 O GLY A 295 SHEET 5 B 7 GLU A 249 ILE A 252 -1 N ILE A 250 O THR A 271 SHEET 6 B 7 VAL A 312 GLY A 314 -1 O GLY A 314 N GLU A 251 SHEET 7 B 7 LYS A 211 PHE A 218 -1 N MET A 212 O VAL A 313 SHEET 1 C 2 LEU A 244 LYS A 245 0 SHEET 2 C 2 GLU A 285 ALA A 286 -1 O ALA A 286 N LEU A 244 SHEET 1 D 2 VAL A 256 PRO A 257 0 SHEET 2 D 2 TYR A 266 GLU A 267 -1 O GLU A 267 N VAL A 256 SHEET 1 E 8 HIS A 331 LEU A 332 0 SHEET 2 E 8 ARG A 402 LYS A 410 -1 O TYR A 406 N HIS A 331 SHEET 3 E 8 ARG A 390 ARG A 395 -1 N ARG A 395 O ARG A 402 SHEET 4 E 8 VAL A 353 VAL A 358 -1 N ASN A 357 O ALA A 392 SHEET 5 E 8 ALA A 361 LEU A 370 -1 O THR A 363 N LEU A 356 SHEET 6 E 8 ILE A 375 CYS A 384 -1 O GLN A 380 N MET A 364 SHEET 7 E 8 VAL A 322 LEU A 328 -1 N LEU A 326 O LEU A 377 SHEET 8 E 8 ARG A 402 LYS A 410 -1 O LYS A 410 N ARG A 327 SHEET 1 F 4 VAL B 37 GLU B 40 0 SHEET 2 F 4 LYS B 43 ILE B 46 -1 O ILE B 45 N THR B 38 SHEET 3 F 4 ARG B 81 LEU B 84 -1 O LEU B 84 N THR B 44 SHEET 4 F 4 GLY B 75 GLU B 78 -1 N GLU B 78 O ARG B 81 SSBOND 1 CYS B 110 CYS B 131 1555 1555 2.90 LINK OG1 THR A 25 MG MG A1001 1555 1555 2.57 LINK SG CYS A 61 ZN ZN A3001 1555 1555 2.10 LINK SG CYS A 64 ZN ZN A3001 1555 1555 2.09 LINK SG CYS A 73 ZN ZN A3001 1555 1555 2.10 LINK SG CYS A 76 ZN ZN A3001 1555 1555 2.10 LINK MG MG A1001 O3B GDP A2001 1555 1555 2.70 LINK MG MG A1001 O HOH A3057 1555 1555 2.24 LINK SG CYS B 107 ZN ZN B3002 1555 1555 2.09 LINK SG CYS B 110 ZN ZN B3002 1555 1555 2.09 LINK SG CYS B 128 ZN ZN B3002 1555 1555 2.09 LINK SG CYS B 131 ZN ZN B3002 1555 1555 2.10 SITE 1 AC1 4 THR A 25 PRO A 92 GDP A2001 HOH A3057 SITE 1 AC2 4 CYS A 61 CYS A 64 CYS A 73 CYS A 76 SITE 1 AC3 4 CYS B 107 CYS B 110 CYS B 128 CYS B 131 SITE 1 AC4 17 HIS A 19 VAL A 20 ASP A 21 GLY A 23 SITE 2 AC4 17 LYS A 24 THR A 25 THR A 26 ASN A 146 SITE 3 AC4 17 LYS A 147 GLU A 149 LEU A 150 SER A 181 SITE 4 AC4 17 ALA A 182 LEU A 183 MG A1001 HOH A3060 SITE 5 AC4 17 HOH A3083 CRYST1 69.198 76.561 97.857 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 0.014451 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013061 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010219 0.00000