HEADER HYDROLASE/RNA 28-OCT-11 3VJR TITLE CRYSTAL STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM ESCHERICHIA COLI IN TITLE 2 COMPLEX WITH THE CCA-ACCEPTOR-T[PSI]C DOMAIN OF TRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-TRNA HYDROLASE; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: PTH; COMPND 5 EC: 3.1.1.29; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TRNA CCA-ACCEPTOR; COMPND 9 CHAIN: B, D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: PTH, B1204, JW1195; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: RNA WAS REPEATED BY IN VITRO TRANSCRIPTION KEYWDS PEPTIDYL-TRNA HYDROLASE, CCA-ACCEPTOR-T[PSI]C DOMAIN, SEVEN BETA- KEYWDS 2 STRANDS FORM, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.ITO,R.MURAKAMI,M.MOCHIZUKI,H.QI,Y.SHIMIZU,K.I.MIURA,T.UEDA, AUTHOR 2 T.UCHIUMI REVDAT 3 08-NOV-23 3VJR 1 SEQADV REVDAT 2 26-JUN-13 3VJR 1 JRNL REVDAT 1 12-SEP-12 3VJR 0 JRNL AUTH K.ITO,R.MURAKAMI,M.MOCHIZUKI,H.QI,Y.SHIMIZU,K.MIURA,T.UEDA, JRNL AUTH 2 T.UCHIUMI JRNL TITL STRUCTURAL BASIS FOR THE SUBSTRATE RECOGNITION AND CATALYSIS JRNL TITL 2 OF PEPTIDYL-TRNA HYDROLASE. JRNL REF NUCLEIC ACIDS RES. V. 40 10521 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22923517 JRNL DOI 10.1093/NAR/GKS790 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26216 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1390 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1865 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2960 REMARK 3 NUCLEIC ACID ATOMS : 1532 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.14000 REMARK 3 B22 (A**2) : 3.14000 REMARK 3 B33 (A**2) : -4.72000 REMARK 3 B12 (A**2) : 1.57000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.243 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.164 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.482 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4734 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6752 ; 1.366 ; 2.371 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 384 ; 5.403 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 132 ;39.940 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 504 ;16.800 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.257 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 810 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3046 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1908 ; 0.488 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3042 ; 0.936 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2826 ; 1.300 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3710 ; 2.025 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 197 REMARK 3 ORIGIN FOR THE GROUP (A): -22.0767 9.7909 1.8265 REMARK 3 T TENSOR REMARK 3 T11: 0.1583 T22: 0.0651 REMARK 3 T33: 0.1091 T12: -0.0843 REMARK 3 T13: 0.0331 T23: -0.0293 REMARK 3 L TENSOR REMARK 3 L11: 1.5136 L22: 2.1424 REMARK 3 L33: 2.3370 L12: 0.0314 REMARK 3 L13: -0.1376 L23: -0.0523 REMARK 3 S TENSOR REMARK 3 S11: -0.1280 S12: 0.0327 S13: -0.0498 REMARK 3 S21: -0.0500 S22: -0.0328 S23: 0.1025 REMARK 3 S31: 0.1958 S32: 0.0641 S33: 0.1608 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 36 REMARK 3 ORIGIN FOR THE GROUP (A): -18.2249 32.5519 -3.2730 REMARK 3 T TENSOR REMARK 3 T11: 0.1711 T22: 0.1066 REMARK 3 T33: 0.1483 T12: -0.0706 REMARK 3 T13: -0.0307 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.5798 L22: 0.4911 REMARK 3 L33: 2.7715 L12: 0.0607 REMARK 3 L13: 0.2617 L23: 1.0366 REMARK 3 S TENSOR REMARK 3 S11: 0.0302 S12: 0.0382 S13: 0.1209 REMARK 3 S21: -0.0403 S22: -0.0637 S23: -0.0696 REMARK 3 S31: -0.2018 S32: -0.2191 S33: 0.0335 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 5 C 197 REMARK 3 ORIGIN FOR THE GROUP (A): -30.1164 23.6566 -40.8329 REMARK 3 T TENSOR REMARK 3 T11: 0.0214 T22: 0.2131 REMARK 3 T33: 0.1143 T12: -0.0020 REMARK 3 T13: 0.0181 T23: -0.0442 REMARK 3 L TENSOR REMARK 3 L11: 2.0477 L22: 1.7453 REMARK 3 L33: 2.2009 L12: -0.1790 REMARK 3 L13: 0.2290 L23: 0.0951 REMARK 3 S TENSOR REMARK 3 S11: -0.0381 S12: -0.0871 S13: -0.0674 REMARK 3 S21: -0.0041 S22: -0.1207 S23: 0.1046 REMARK 3 S31: -0.1642 S32: -0.1366 S33: 0.1588 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 36 REMARK 3 ORIGIN FOR THE GROUP (A): -8.3464 15.5810 -35.8746 REMARK 3 T TENSOR REMARK 3 T11: 0.1107 T22: 0.2262 REMARK 3 T33: 0.1663 T12: -0.0043 REMARK 3 T13: 0.0131 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 0.5600 L22: 0.2889 REMARK 3 L33: 2.4748 L12: 0.1822 REMARK 3 L13: -1.0296 L23: -0.2584 REMARK 3 S TENSOR REMARK 3 S11: -0.0676 S12: 0.0038 S13: 0.0179 REMARK 3 S21: 0.0541 S22: 0.0151 S23: -0.1417 REMARK 3 S31: 0.3393 S32: 0.0477 S33: 0.0525 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 : 1.40 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 3VJR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000095131. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27129 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : 24.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.18700 REMARK 200 R SYM FOR SHELL (I) : 0.20000 REMARK 200 FOR SHELL : 8.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2PTH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM ACETATE BUFFER, 20% (W/V) 1,4 REMARK 280 -BUTANEDIOL, 30MM GLYCYL-GLYCYL-GLYCINE , PH 5.2, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 137.70000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 275.40000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 206.55000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 344.25000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.85000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 MET A 4 REMARK 465 GLY C 1 REMARK 465 SER C 2 REMARK 465 HIS C 3 REMARK 465 MET C 4 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 G B 1 P G B 1 OP3 -0.136 REMARK 500 G D 1 P G D 1 OP3 -0.143 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 G B 2 C4' - C3' - C2' ANGL. DEV. = -7.5 DEGREES REMARK 500 C B 31 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 G D 2 C4' - C3' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 C D 6 O4' - C1' - N1 ANGL. DEV. = 4.5 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 ASP C 90 1.01 -69.91 REMARK 500 LYS C 148 32.76 -99.22 REMARK 500 REMARK 500 REMARK: NULL DBREF 3VJR A 4 197 UNP P0A7D1 PTH_ECOLI 1 194 DBREF 3VJR C 4 197 UNP P0A7D1 PTH_ECOLI 1 194 DBREF 3VJR B 1 36 PDB 3VJR 3VJR 1 36 DBREF 3VJR D 1 36 PDB 3VJR 3VJR 1 36 SEQADV 3VJR GLY A 1 UNP P0A7D1 EXPRESSION TAG SEQADV 3VJR SER A 2 UNP P0A7D1 EXPRESSION TAG SEQADV 3VJR HIS A 3 UNP P0A7D1 EXPRESSION TAG SEQADV 3VJR GLY C 1 UNP P0A7D1 EXPRESSION TAG SEQADV 3VJR SER C 2 UNP P0A7D1 EXPRESSION TAG SEQADV 3VJR HIS C 3 UNP P0A7D1 EXPRESSION TAG SEQRES 1 A 197 GLY SER HIS MET THR ILE LYS LEU ILE VAL GLY LEU ALA SEQRES 2 A 197 ASN PRO GLY ALA GLU TYR ALA ALA THR ARG HIS ASN ALA SEQRES 3 A 197 GLY ALA TRP PHE VAL ASP LEU LEU ALA GLU ARG LEU ARG SEQRES 4 A 197 ALA PRO LEU ARG GLU GLU ALA LYS PHE PHE GLY TYR THR SEQRES 5 A 197 SER ARG VAL THR LEU GLY GLY GLU ASP VAL ARG LEU LEU SEQRES 6 A 197 VAL PRO THR THR PHE MET ASN LEU SER GLY LYS ALA VAL SEQRES 7 A 197 ALA ALA MET ALA SER PHE PHE ARG ILE ASN PRO ASP GLU SEQRES 8 A 197 ILE LEU VAL ALA HIS ASP GLU LEU ASP LEU PRO PRO GLY SEQRES 9 A 197 VAL ALA LYS PHE LYS LEU GLY GLY GLY HIS GLY GLY HIS SEQRES 10 A 197 ASN GLY LEU LYS ASP ILE ILE SER LYS LEU GLY ASN ASN SEQRES 11 A 197 PRO ASN PHE HIS ARG LEU ARG ILE GLY ILE GLY HIS PRO SEQRES 12 A 197 GLY ASP LYS ASN LYS VAL VAL GLY PHE VAL LEU GLY LYS SEQRES 13 A 197 PRO PRO VAL SER GLU GLN LYS LEU ILE ASP GLU ALA ILE SEQRES 14 A 197 ASP GLU ALA ALA ARG CYS THR GLU MET TRP PHE THR ASP SEQRES 15 A 197 GLY LEU THR LYS ALA THR ASN ARG LEU HIS ALA PHE LYS SEQRES 16 A 197 ALA GLN SEQRES 1 B 36 G G G G G C U A A G C G G SEQRES 2 B 36 U U C G A U C C C G C U U SEQRES 3 B 36 A G C U C C A C C A SEQRES 1 C 197 GLY SER HIS MET THR ILE LYS LEU ILE VAL GLY LEU ALA SEQRES 2 C 197 ASN PRO GLY ALA GLU TYR ALA ALA THR ARG HIS ASN ALA SEQRES 3 C 197 GLY ALA TRP PHE VAL ASP LEU LEU ALA GLU ARG LEU ARG SEQRES 4 C 197 ALA PRO LEU ARG GLU GLU ALA LYS PHE PHE GLY TYR THR SEQRES 5 C 197 SER ARG VAL THR LEU GLY GLY GLU ASP VAL ARG LEU LEU SEQRES 6 C 197 VAL PRO THR THR PHE MET ASN LEU SER GLY LYS ALA VAL SEQRES 7 C 197 ALA ALA MET ALA SER PHE PHE ARG ILE ASN PRO ASP GLU SEQRES 8 C 197 ILE LEU VAL ALA HIS ASP GLU LEU ASP LEU PRO PRO GLY SEQRES 9 C 197 VAL ALA LYS PHE LYS LEU GLY GLY GLY HIS GLY GLY HIS SEQRES 10 C 197 ASN GLY LEU LYS ASP ILE ILE SER LYS LEU GLY ASN ASN SEQRES 11 C 197 PRO ASN PHE HIS ARG LEU ARG ILE GLY ILE GLY HIS PRO SEQRES 12 C 197 GLY ASP LYS ASN LYS VAL VAL GLY PHE VAL LEU GLY LYS SEQRES 13 C 197 PRO PRO VAL SER GLU GLN LYS LEU ILE ASP GLU ALA ILE SEQRES 14 C 197 ASP GLU ALA ALA ARG CYS THR GLU MET TRP PHE THR ASP SEQRES 15 C 197 GLY LEU THR LYS ALA THR ASN ARG LEU HIS ALA PHE LYS SEQRES 16 C 197 ALA GLN SEQRES 1 D 36 G G G G G C U A A G C G G SEQRES 2 D 36 U U C G A U C C C G C U U SEQRES 3 D 36 A G C U C C A C C A FORMUL 5 HOH *139(H2 O) HELIX 1 1 THR A 22 HIS A 24 5 3 HELIX 2 2 ASN A 25 LEU A 38 1 14 HELIX 3 3 ALA A 46 PHE A 48 5 3 HELIX 4 4 PHE A 70 ASN A 72 5 3 HELIX 5 5 LEU A 73 ARG A 86 1 14 HELIX 6 6 ASN A 88 ASP A 90 5 3 HELIX 7 7 HIS A 117 LEU A 127 1 11 HELIX 8 8 ASP A 145 ASN A 147 5 3 HELIX 9 9 LYS A 148 LEU A 154 1 7 HELIX 10 10 PRO A 158 GLY A 183 1 26 HELIX 11 11 GLY A 183 HIS A 192 1 10 HELIX 12 12 GLY C 16 ALA C 20 5 5 HELIX 13 13 THR C 22 HIS C 24 5 3 HELIX 14 14 ASN C 25 LEU C 38 1 14 HELIX 15 15 ALA C 46 PHE C 48 5 3 HELIX 16 16 PHE C 70 ASN C 72 5 3 HELIX 17 17 LEU C 73 ARG C 86 1 14 HELIX 18 18 ASN C 88 ASP C 90 5 3 HELIX 19 19 HIS C 117 LEU C 127 1 11 HELIX 20 20 ASP C 145 ASN C 147 5 3 HELIX 21 21 LYS C 148 LEU C 154 1 7 HELIX 22 22 PRO C 158 GLY C 183 1 26 HELIX 23 23 GLY C 183 HIS C 192 1 10 SHEET 1 A 7 ARG A 43 GLU A 45 0 SHEET 2 A 7 GLY A 50 LEU A 57 -1 O GLY A 50 N GLU A 45 SHEET 3 A 7 GLU A 60 PRO A 67 -1 O VAL A 62 N VAL A 55 SHEET 4 A 7 LEU A 8 GLY A 11 1 N GLY A 11 O LEU A 65 SHEET 5 A 7 ILE A 92 GLU A 98 1 O ALA A 95 N VAL A 10 SHEET 6 A 7 HIS A 134 GLY A 139 1 O ILE A 138 N HIS A 96 SHEET 7 A 7 ALA A 106 LEU A 110 -1 N LYS A 107 O ARG A 137 SHEET 1 B 7 ARG C 43 GLU C 45 0 SHEET 2 B 7 GLY C 50 LEU C 57 -1 O GLY C 50 N GLU C 45 SHEET 3 B 7 GLU C 60 PRO C 67 -1 O VAL C 62 N VAL C 55 SHEET 4 B 7 LEU C 8 GLY C 11 1 N ILE C 9 O ARG C 63 SHEET 5 B 7 ILE C 92 GLU C 98 1 O ALA C 95 N VAL C 10 SHEET 6 B 7 HIS C 134 GLY C 139 1 O ILE C 138 N GLU C 98 SHEET 7 B 7 ALA C 106 LEU C 110 -1 N LYS C 107 O ARG C 137 CRYST1 55.070 55.070 413.100 90.00 90.00 120.00 P 61 12 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 0.018159 0.010484 0.000000 0.00000 SCALE2 0.000000 0.020968 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002421 0.00000