HEADER TRANSLATION 04-OCT-18 6HTW TITLE CRYSTAL STRUCTURE OF AN ANCIENT SEQUENCE-RECONSTRUCTED ELONGATION TITLE 2 FACTOR TU (NODE 184) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ELONGATION FACTOR TU; COMPND 3 CHAIN: H, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN SYNTHESIS, ELONGATION FACTOR, SEQUENCE RECONSTRUCTION, KEYWDS 2 ANCIENT PROTEIN, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR S.MAJUMDAR,T.BERGFORS,S.SANYAL REVDAT 2 24-JAN-24 6HTW 1 LINK REVDAT 1 23-OCT-19 6HTW 0 JRNL AUTH S.MAJUMDAR,T.BERGFORS,S.SANYAL JRNL TITL CRYSTAL STRUCTURE OF AN ANCIENT SEQUENCE-RECONSTRUCTED JRNL TITL 2 ELONGATION FACTOR TU (NODE 184) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 112.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 87124 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4510 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6262 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.3480 REMARK 3 BIN FREE R VALUE SET COUNT : 364 REMARK 3 BIN FREE R VALUE : 0.3620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5684 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.64000 REMARK 3 B22 (A**2) : 1.03000 REMARK 3 B33 (A**2) : -1.66000 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): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.116 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.462 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5848 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5595 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7946 ; 2.037 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12874 ; 1.059 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 738 ; 6.933 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 254 ;36.355 ;23.937 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 982 ;14.342 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;19.587 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 912 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6553 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1237 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6HTW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1200012286. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.23 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91686 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 112.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 1.81900 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: AUTO-RICKSHAW REMARK 200 STARTING MODEL: 1EFC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 8000, 20% ETHYLENE GLYCOL, 20 REMARK 280 MM EACH OF 1,6-HEXANEDIOL, 1-BUTANOL 1-2-PROPANEDIOL 2-PROPANOL REMARK 280 1,4-BUTAEDIOL 1,3-PROPANEDIOL AND 0.1 MM MES/IMIDAZOLE, PH6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 41.10150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.06100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.10150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.06100 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: 2730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, 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 ALA H 37 REMARK 465 ALA H 38 REMARK 465 LYS H 39 REMARK 465 GLY H 40 REMARK 465 LYS H 41 REMARK 465 ALA H 42 REMARK 465 GLU H 43 REMARK 465 ALA H 44 REMARK 465 ARG H 45 REMARK 465 ALA H 46 REMARK 465 TYR H 47 REMARK 465 ASP H 48 REMARK 465 GLN H 49 REMARK 465 ILE H 50 REMARK 465 ASP H 51 REMARK 465 LYS H 52 REMARK 465 ALA H 53 REMARK 465 PRO H 54 REMARK 465 GLU H 55 REMARK 465 GLU H 56 REMARK 465 LYS H 57 REMARK 465 ALA H 58 REMARK 465 ARG H 59 REMARK 465 GLY H 60 REMARK 465 ILE H 61 REMARK 465 THR H 62 REMARK 465 ILE H 63 REMARK 465 ASN H 64 REMARK 465 GLU H 394 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 HIS H 85 CB CG ND1 CD2 CE1 NE2 REMARK 470 ALA H 86 CB REMARK 470 ALA H 96 CB REMARK 470 ALA H 97 CB REMARK 470 GLN H 98 CG CD OE1 NE2 REMARK 470 MET H 140 SD CE REMARK 470 GLU H 145 CG CD OE1 OE2 REMARK 470 LEU H 146 CG CD1 CD2 REMARK 470 LEU H 149 CG CD1 CD2 REMARK 470 MET H 152 CG SD CE REMARK 470 ASN H 183 CG OD1 ND2 REMARK 470 GLU H 285 CG CD OE1 OE2 REMARK 470 LYS H 314 CG CD CE NZ REMARK 470 GLU H 315 CG CD OE1 OE2 REMARK 470 GLU H 346 CG CD OE1 OE2 REMARK 470 GLU H 349 CB CG CD OE1 OE2 REMARK 470 GLN B 98 CG CD OE1 NE2 REMARK 470 MET B 152 SD CE REMARK 470 LYS B 177 CE NZ 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 OE2 GLU B 371 O HOH B 501 2.19 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 ARG H 75 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 TYR H 161 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG H 231 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG H 234 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG H 234 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP B 167 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 MET B 193 CG - SD - CE ANGL. DEV. = -16.1 DEGREES REMARK 500 ARG B 224 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 289 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 334 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 334 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG B 378 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 378 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 382 NE - CZ - NH2 ANGL. DEV. = -3.2 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 H 85 -130.15 55.13 REMARK 500 ALA H 97 -61.69 -98.76 REMARK 500 GLN H 98 94.42 80.46 REMARK 500 TYR H 161 -149.02 -97.37 REMARK 500 GLU H 180 14.23 -65.59 REMARK 500 ARG H 224 -90.57 -127.75 REMARK 500 LEU H 248 -32.35 73.23 REMARK 500 LYS H 264 -39.61 -132.61 REMARK 500 ASP H 267 -24.53 83.24 REMARK 500 ARG H 334 -106.99 51.92 REMARK 500 ALA B 58 66.83 -64.03 REMARK 500 ARG B 59 79.48 60.14 REMARK 500 THR B 94 27.82 -143.80 REMARK 500 ARG B 224 -51.74 -132.97 REMARK 500 LEU B 248 -26.81 65.95 REMARK 500 ARG B 334 -67.46 65.86 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 H 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR H 26 OG1 REMARK 620 2 GDP H 401 O2B 88.7 REMARK 620 3 HOH H 507 O 88.4 98.3 REMARK 620 4 HOH H 529 O 82.3 85.5 169.9 REMARK 620 5 HOH H 597 O 87.5 172.6 87.9 87.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 26 OG1 REMARK 620 2 GDP B 401 O2B 93.5 REMARK 620 3 HOH B 503 O 95.4 78.6 REMARK 620 4 HOH B 525 O 82.5 100.0 177.4 REMARK 620 5 HOH B 532 O 169.8 94.1 92.7 89.5 REMARK 620 6 HOH B 611 O 84.3 170.4 92.3 88.9 89.2 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 GDP H 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG H 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6GFU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN ANCIENT SEQUENCE-RECONSTRUCTED ELONGATION REMARK 900 FACTOR TU (NODE 262) DBREF 6HTW H 10 394 PDB 6HTW 6HTW 10 394 DBREF 6HTW B 10 394 PDB 6HTW 6HTW 10 394 SEQRES 1 H 385 LYS PRO HIS VAL ASN ILE GLY THR ILE GLY HIS VAL ASP SEQRES 2 H 385 HIS GLY LYS THR THR LEU THR ALA ALA ILE THR LYS THR SEQRES 3 H 385 LEU ALA ALA LYS GLY LYS ALA GLU ALA ARG ALA TYR ASP SEQRES 4 H 385 GLN ILE ASP LYS ALA PRO GLU GLU LYS ALA ARG GLY ILE SEQRES 5 H 385 THR ILE ASN THR ALA HIS VAL GLU TYR GLU THR GLU ASN SEQRES 6 H 385 ARG HIS TYR ALA HIS VAL ASP CYS PRO GLY HIS ALA ASP SEQRES 7 H 385 TYR VAL LYS ASN MET ILE THR GLY ALA ALA GLN MET ASP SEQRES 8 H 385 GLY ALA ILE LEU VAL VAL SER ALA ALA ASP GLY PRO MET SEQRES 9 H 385 PRO GLN THR ARG GLU HIS ILE LEU LEU ALA ARG GLN VAL SEQRES 10 H 385 GLY VAL PRO TYR ILE VAL VAL PHE LEU ASN LYS CYS ASP SEQRES 11 H 385 MET VAL ASP ASP GLU GLU LEU LEU GLU LEU VAL GLU MET SEQRES 12 H 385 GLU VAL ARG GLU LEU LEU SER GLU TYR GLU PHE PRO GLY SEQRES 13 H 385 ASP ASP ILE PRO ILE ILE ARG GLY SER ALA LEU LYS ALA SEQRES 14 H 385 LEU GLU GLY GLU ASN GLU TRP VAL ASP LYS ILE TRP GLU SEQRES 15 H 385 LEU MET ASP ALA VAL ASP SER TYR ILE PRO THR PRO GLU SEQRES 16 H 385 ARG ASP VAL ASP LYS PRO PHE LEU MET PRO VAL GLU ASP SEQRES 17 H 385 VAL PHE THR ILE THR GLY ARG GLY THR VAL ALA THR GLY SEQRES 18 H 385 ARG VAL GLU ARG GLY THR VAL LYS VAL GLY ASP GLU VAL SEQRES 19 H 385 GLU ILE VAL GLY LEU ARG ASP THR ARG LYS THR VAL VAL SEQRES 20 H 385 THR GLY VAL GLU MET PHE ARG LYS LEU LEU ASP GLU GLY SEQRES 21 H 385 MET ALA GLY ASP ASN VAL GLY VAL LEU LEU ARG GLY ILE SEQRES 22 H 385 GLN ARG GLU ASP VAL GLU ARG GLY GLN VAL LEU ALA LYS SEQRES 23 H 385 PRO GLY SER ILE LYS PRO HIS THR LYS PHE GLU ALA GLU SEQRES 24 H 385 VAL TYR VAL LEU THR LYS GLU GLU GLY GLY ARG HIS THR SEQRES 25 H 385 PRO PHE PHE ASN GLY TYR ARG PRO GLN PHE TYR PHE ARG SEQRES 26 H 385 THR THR ASP VAL THR GLY VAL ILE THR LEU PRO GLU GLY SEQRES 27 H 385 VAL GLU MET VAL MET PRO GLY ASP ASN VAL THR MET THR SEQRES 28 H 385 VAL GLU LEU ILE HIS PRO ILE ALA MET GLU GLU GLY LEU SEQRES 29 H 385 ARG PHE ALA ILE ARG GLU GLY GLY ARG THR VAL GLY ALA SEQRES 30 H 385 GLY VAL VAL SER LYS ILE ILE GLU SEQRES 1 B 385 LYS PRO HIS VAL ASN ILE GLY THR ILE GLY HIS VAL ASP SEQRES 2 B 385 HIS GLY LYS THR THR LEU THR ALA ALA ILE THR LYS THR SEQRES 3 B 385 LEU ALA ALA LYS GLY LYS ALA GLU ALA ARG ALA TYR ASP SEQRES 4 B 385 GLN ILE ASP LYS ALA PRO GLU GLU LYS ALA ARG GLY ILE SEQRES 5 B 385 THR ILE ASN THR ALA HIS VAL GLU TYR GLU THR GLU ASN SEQRES 6 B 385 ARG HIS TYR ALA HIS VAL ASP CYS PRO GLY HIS ALA ASP SEQRES 7 B 385 TYR VAL LYS ASN MET ILE THR GLY ALA ALA GLN MET ASP SEQRES 8 B 385 GLY ALA ILE LEU VAL VAL SER ALA ALA ASP GLY PRO MET SEQRES 9 B 385 PRO GLN THR ARG GLU HIS ILE LEU LEU ALA ARG GLN VAL SEQRES 10 B 385 GLY VAL PRO TYR ILE VAL VAL PHE LEU ASN LYS CYS ASP SEQRES 11 B 385 MET VAL ASP ASP GLU GLU LEU LEU GLU LEU VAL GLU MET SEQRES 12 B 385 GLU VAL ARG GLU LEU LEU SER GLU TYR GLU PHE PRO GLY SEQRES 13 B 385 ASP ASP ILE PRO ILE ILE ARG GLY SER ALA LEU LYS ALA SEQRES 14 B 385 LEU GLU GLY GLU ASN GLU TRP VAL ASP LYS ILE TRP GLU SEQRES 15 B 385 LEU MET ASP ALA VAL ASP SER TYR ILE PRO THR PRO GLU SEQRES 16 B 385 ARG ASP VAL ASP LYS PRO PHE LEU MET PRO VAL GLU ASP SEQRES 17 B 385 VAL PHE THR ILE THR GLY ARG GLY THR VAL ALA THR GLY SEQRES 18 B 385 ARG VAL GLU ARG GLY THR VAL LYS VAL GLY ASP GLU VAL SEQRES 19 B 385 GLU ILE VAL GLY LEU ARG ASP THR ARG LYS THR VAL VAL SEQRES 20 B 385 THR GLY VAL GLU MET PHE ARG LYS LEU LEU ASP GLU GLY SEQRES 21 B 385 MET ALA GLY ASP ASN VAL GLY VAL LEU LEU ARG GLY ILE SEQRES 22 B 385 GLN ARG GLU ASP VAL GLU ARG GLY GLN VAL LEU ALA LYS SEQRES 23 B 385 PRO GLY SER ILE LYS PRO HIS THR LYS PHE GLU ALA GLU SEQRES 24 B 385 VAL TYR VAL LEU THR LYS GLU GLU GLY GLY ARG HIS THR SEQRES 25 B 385 PRO PHE PHE ASN GLY TYR ARG PRO GLN PHE TYR PHE ARG SEQRES 26 B 385 THR THR ASP VAL THR GLY VAL ILE THR LEU PRO GLU GLY SEQRES 27 B 385 VAL GLU MET VAL MET PRO GLY ASP ASN VAL THR MET THR SEQRES 28 B 385 VAL GLU LEU ILE HIS PRO ILE ALA MET GLU GLU GLY LEU SEQRES 29 B 385 ARG PHE ALA ILE ARG GLU GLY GLY ARG THR VAL GLY ALA SEQRES 30 B 385 GLY VAL VAL SER LYS ILE ILE GLU HET GDP H 401 28 HET MG H 402 1 HET GDP B 401 28 HET MG B 402 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 GDP 2(C10 H15 N5 O11 P2) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *450(H2 O) HELIX 1 AA1 GLY H 24 THR H 35 1 12 HELIX 2 AA2 HIS H 85 GLY H 95 1 11 HELIX 3 AA3 MET H 113 VAL H 126 1 14 HELIX 4 AA4 LYS H 137 VAL H 141 5 5 HELIX 5 AA5 ASP H 143 TYR H 161 1 19 HELIX 6 AA6 SER H 174 GLU H 180 1 7 HELIX 7 AA7 GLU H 182 ILE H 200 1 19 HELIX 8 AA8 ARG H 205 LYS H 209 5 5 HELIX 9 AA9 GLN H 283 VAL H 287 5 5 HELIX 10 AB1 THR H 313 GLY H 317 5 5 HELIX 11 AB2 GLY B 24 ALA B 38 1 15 HELIX 12 AB3 ALA B 46 LYS B 52 1 7 HELIX 13 AB4 GLY B 84 GLY B 95 1 12 HELIX 14 AB5 MET B 113 VAL B 126 1 14 HELIX 15 AB6 LYS B 137 VAL B 141 5 5 HELIX 16 AB7 ASP B 143 TYR B 161 1 19 HELIX 17 AB8 SER B 174 GLY B 181 1 8 HELIX 18 AB9 GLU B 182 ILE B 200 1 19 HELIX 19 AC1 ARG B 205 LYS B 209 5 5 HELIX 20 AC2 GLN B 283 VAL B 287 5 5 SHEET 1 AA1 6 ALA H 66 GLU H 71 0 SHEET 2 AA1 6 HIS H 76 ASP H 81 -1 O TYR H 77 N TYR H 70 SHEET 3 AA1 6 HIS H 12 ILE H 18 1 N ILE H 15 O ALA H 78 SHEET 4 AA1 6 GLY H 101 SER H 107 1 O ILE H 103 N GLY H 16 SHEET 5 AA1 6 ILE H 131 ASN H 136 1 O PHE H 134 N LEU H 104 SHEET 6 AA1 6 ILE H 170 ARG H 172 1 O ILE H 171 N LEU H 135 SHEET 1 AA2 7 LEU H 212 PRO H 214 0 SHEET 2 AA2 7 VAL H 292 ALA H 294 -1 O LEU H 293 N MET H 213 SHEET 3 AA2 7 GLU H 242 VAL H 246 -1 N GLU H 244 O ALA H 294 SHEET 4 AA2 7 ARG H 252 MET H 261 -1 O THR H 254 N VAL H 243 SHEET 5 AA2 7 ASN H 274 LEU H 279 -1 O GLY H 276 N GLU H 260 SHEET 6 AA2 7 GLY H 225 ARG H 231 -1 N ALA H 228 O VAL H 277 SHEET 7 AA2 7 ASP H 217 ILE H 221 -1 N PHE H 219 O VAL H 227 SHEET 1 AA3 5 LEU H 212 PRO H 214 0 SHEET 2 AA3 5 VAL H 292 ALA H 294 -1 O LEU H 293 N MET H 213 SHEET 3 AA3 5 GLU H 242 VAL H 246 -1 N GLU H 244 O ALA H 294 SHEET 4 AA3 5 ARG H 252 MET H 261 -1 O THR H 254 N VAL H 243 SHEET 5 AA3 5 LEU H 265 LEU H 266 -1 O LEU H 265 N MET H 261 SHEET 1 AA4 2 THR H 236 LYS H 238 0 SHEET 2 AA4 2 GLU H 268 MET H 270 -1 O GLY H 269 N VAL H 237 SHEET 1 AA5 7 PRO H 301 VAL H 311 0 SHEET 2 AA5 7 ASN H 356 ALA H 368 -1 O VAL H 357 N VAL H 309 SHEET 3 AA5 7 THR H 336 THR H 343 -1 N THR H 339 O ILE H 364 SHEET 4 AA5 7 GLN H 330 PHE H 333 -1 N PHE H 331 O VAL H 338 SHEET 5 AA5 7 ARG H 374 ARG H 378 -1 O ALA H 376 N TYR H 332 SHEET 6 AA5 7 THR H 383 ILE H 392 -1 O GLY H 387 N PHE H 375 SHEET 7 AA5 7 PRO H 301 VAL H 311 -1 N GLU H 306 O LYS H 391 SHEET 1 AA6 2 PHE H 323 PHE H 324 0 SHEET 2 AA6 2 MET H 350 VAL H 351 -1 O VAL H 351 N PHE H 323 SHEET 1 AA7 6 ALA B 66 GLU B 71 0 SHEET 2 AA7 6 HIS B 76 ASP B 81 -1 O TYR B 77 N TYR B 70 SHEET 3 AA7 6 HIS B 12 ILE B 18 1 N ILE B 15 O ALA B 78 SHEET 4 AA7 6 ALA B 102 SER B 107 1 O ILE B 103 N GLY B 16 SHEET 5 AA7 6 ILE B 131 ASN B 136 1 O VAL B 132 N LEU B 104 SHEET 6 AA7 6 ILE B 170 ARG B 172 1 O ILE B 171 N LEU B 135 SHEET 1 AA8 2 GLU B 55 ALA B 58 0 SHEET 2 AA8 2 ILE B 61 ASN B 64 -1 O ILE B 63 N GLU B 56 SHEET 1 AA9 7 LEU B 212 PRO B 214 0 SHEET 2 AA9 7 VAL B 292 ALA B 294 -1 O LEU B 293 N MET B 213 SHEET 3 AA9 7 GLU B 242 VAL B 246 -1 N GLU B 244 O ALA B 294 SHEET 4 AA9 7 ARG B 252 MET B 261 -1 O THR B 254 N VAL B 243 SHEET 5 AA9 7 ASN B 274 LEU B 279 -1 O GLY B 276 N GLU B 260 SHEET 6 AA9 7 GLY B 225 ARG B 231 -1 N GLY B 230 O VAL B 275 SHEET 7 AA9 7 ASP B 217 ILE B 221 -1 N PHE B 219 O VAL B 227 SHEET 1 AB1 5 LEU B 212 PRO B 214 0 SHEET 2 AB1 5 VAL B 292 ALA B 294 -1 O LEU B 293 N MET B 213 SHEET 3 AB1 5 GLU B 242 VAL B 246 -1 N GLU B 244 O ALA B 294 SHEET 4 AB1 5 ARG B 252 MET B 261 -1 O THR B 254 N VAL B 243 SHEET 5 AB1 5 LYS B 264 LEU B 265 -1 O LYS B 264 N MET B 261 SHEET 1 AB2 2 THR B 236 VAL B 237 0 SHEET 2 AB2 2 GLY B 269 MET B 270 -1 O GLY B 269 N VAL B 237 SHEET 1 AB3 7 LYS B 300 VAL B 311 0 SHEET 2 AB3 7 ASN B 356 MET B 369 -1 O LEU B 363 N THR B 303 SHEET 3 AB3 7 THR B 336 THR B 343 -1 N THR B 343 O THR B 360 SHEET 4 AB3 7 GLN B 330 PHE B 333 -1 N PHE B 333 O THR B 336 SHEET 5 AB3 7 ARG B 374 GLU B 379 -1 O ALA B 376 N TYR B 332 SHEET 6 AB3 7 ARG B 382 ILE B 392 -1 O GLY B 387 N PHE B 375 SHEET 7 AB3 7 LYS B 300 VAL B 311 -1 N TYR B 310 O ALA B 386 SHEET 1 AB4 2 PHE B 323 PHE B 324 0 SHEET 2 AB4 2 MET B 350 VAL B 351 -1 O VAL B 351 N PHE B 323 LINK OG1 THR H 26 MG MG H 402 1555 1555 1.94 LINK O2B GDP H 401 MG MG H 402 1555 1555 2.19 LINK MG MG H 402 O HOH H 507 1555 1555 2.14 LINK MG MG H 402 O HOH H 529 1555 1555 2.01 LINK MG MG H 402 O HOH H 597 1555 1555 2.11 LINK OG1 THR B 26 MG MG B 402 1555 1555 2.01 LINK O2B GDP B 401 MG MG B 402 1555 1555 2.00 LINK MG MG B 402 O HOH B 503 1555 1555 2.22 LINK MG MG B 402 O HOH B 525 1555 1555 2.15 LINK MG MG B 402 O HOH B 532 1555 1555 2.12 LINK MG MG B 402 O HOH B 611 1555 1555 2.13 SITE 1 AC1 16 VAL H 21 ASP H 22 HIS H 23 GLY H 24 SITE 2 AC1 16 LYS H 25 THR H 26 THR H 27 ASN H 136 SITE 3 AC1 16 LYS H 137 ASP H 139 MET H 140 SER H 174 SITE 4 AC1 16 ALA H 175 LEU H 176 MG H 402 HOH H 529 SITE 1 AC2 5 THR H 26 GDP H 401 HOH H 507 HOH H 529 SITE 2 AC2 5 HOH H 597 SITE 1 AC3 20 HIS B 20 ASP B 22 HIS B 23 GLY B 24 SITE 2 AC3 20 LYS B 25 THR B 26 THR B 27 TYR B 47 SITE 3 AC3 20 ASN B 136 LYS B 137 ASP B 139 MET B 140 SITE 4 AC3 20 SER B 174 ALA B 175 LEU B 176 MG B 402 SITE 5 AC3 20 HOH B 503 HOH B 516 HOH B 532 HOH B 557 SITE 1 AC4 6 THR B 26 GDP B 401 HOH B 503 HOH B 525 SITE 2 AC4 6 HOH B 532 HOH B 611 CRYST1 82.203 106.122 112.472 90.00 90.00 90.00 P 21 21 2 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 0.012165 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009423 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008891 0.00000