HEADER HYDROLASE/RNA 31-JUL-12 4GCW TITLE CRYSTAL STRUCTURE OF RNASE Z IN COMPLEX WITH PRECURSOR TRNA(THR) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE Z; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE Z, TRNA 3 ENDONUCLEASE, TRNASE Z; COMPND 5 EC: 3.1.26.11; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TRNA(THR); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: BSU23840, RNZ, YQJK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: B.SUBTILIS TRNATHR(ENCODED BY THE TRN1-THR GENE) WAS SOURCE 14 SYNTHETISED AS A PRECURSOR WITH 2 NT 3'-EXTENSION. THE NT 73-76 ARE SOURCE 15 2'-O-METHYLATED. KEYWDS ZINC-DEPENDENT METALO BETALACTAMASE - RNA COMPLEX, TRNA MATURASE, KEYWDS 2 PROTEIN-RNA COMPLEX, TRNA BINDING, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR O.PELLEGRINI,I.LI DE LA SIERRA-GALLAY,J.PITON,L.GILET,C.CONDON REVDAT 2 13-SEP-23 4GCW 1 REMARK SEQADV LINK REVDAT 1 31-OCT-12 4GCW 0 JRNL AUTH O.PELLEGRINI,I.LI DE LA SIERRA-GALLAY,J.PITON,L.GILET, JRNL AUTH 2 C.CONDON JRNL TITL ACTIVATION OF TRNA MATURATION BY DOWNSTREAM URACIL RESIDUES JRNL TITL 2 IN B. SUBTILIS JRNL REF STRUCTURE V. 20 1769 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 22940585 JRNL DOI 10.1016/J.STR.2012.08.002 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 13230 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 662 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 : 7 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.24 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.09 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2677 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2564 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2543 REMARK 3 BIN R VALUE (WORKING SET) : 0.2554 REMARK 3 BIN FREE R VALUE : 0.2763 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.01 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 134 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 : 2400 REMARK 3 NUCLEIC ACID ATOMS : 1172 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 32 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 82.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 31.79380 REMARK 3 B22 (A**2) : -7.41070 REMARK 3 B33 (A**2) : -24.38310 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 8.07380 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.476 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.845 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.839 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3767 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5350 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1514 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 61 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 409 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3767 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : NULL ; NULL ; NULL REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : NULL ; NULL ; NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.07 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL REMARK 3 OTHER TORSION ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4GCW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074024. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 REMARK 200 MONOCHROMATOR : CRYOGENICALLY COOLED REMARK 200 MONOCHROMATOR CRYSTAL REMARK 200 OPTICS : KIRK PATRICK-BAEZ PAIR OF BI REMARK 200 -MORPH MIRRORS PLUS CHANNEL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS PACKAGE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13408 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.980 REMARK 200 RESOLUTION RANGE LOW (A) : 43.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.71600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.060 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 2FK6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG MME 2K, 0.1 M NA-MES, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 87.04000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.27500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 87.04000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.27500 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, 3 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: 3240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -91.0 KCAL/MOL 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -67.01316 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 88.35060 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -216.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -67.01316 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 88.35060 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 LYS A 308 REMARK 465 LEU A 309 REMARK 465 ALA A 310 REMARK 465 ALA A 311 REMARK 465 ALA A 312 REMARK 465 LEU A 313 REMARK 465 GLU A 314 REMARK 465 HIS A 315 REMARK 465 HIS A 316 REMARK 465 HIS A 317 REMARK 465 HIS A 318 REMARK 465 HIS A 319 REMARK 465 HIS A 320 REMARK 465 C B 27 REMARK 465 U B 28 REMARK 465 U B 29 REMARK 465 C B 30 REMARK 465 C B 31 REMARK 465 A B 32 REMARK 465 U B 33 REMARK 465 G B 34 REMARK 465 G B 35 REMARK 465 U B 36 REMARK 465 A B 37 REMARK 465 A B 38 REMARK 465 G B 39 REMARK 465 G B 40 REMARK 465 A B 41 REMARK 465 A B 42 REMARK 465 G B 43 REMARK 465 A B 44 REMARK 465 G B 45 REMARK 465 A2M B 75 REMARK 465 A2M B 76 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 G B 46 P OP1 OP2 O5' 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 U B 3 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 A B 9 C3' - O3' - P ANGL. DEV. = 13.2 DEGREES REMARK 500 C B 11 C3' - O3' - P ANGL. DEV. = 11.4 DEGREES REMARK 500 U B 12 C3' - O3' - P ANGL. DEV. = 12.7 DEGREES REMARK 500 C B 13 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 A B 21 C3' - O3' - P ANGL. DEV. = 11.7 DEGREES REMARK 500 G B 46 C3' - O3' - P ANGL. DEV. = 11.3 DEGREES REMARK 500 OMU B 73 O3' - P - O5' ANGL. DEV. = 12.6 DEGREES REMARK 500 OMU B 73 C3' - O3' - P ANGL. DEV. = 30.1 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 THR A 20 125.69 -37.76 REMARK 500 SER A 21 116.92 -177.59 REMARK 500 ARG A 30 20.66 -147.74 REMARK 500 ASP A 37 139.28 75.83 REMARK 500 MET A 64 0.61 -65.01 REMARK 500 TYR A 70 -4.49 -54.03 REMARK 500 GLU A 143 99.85 -63.99 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 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 63 NE2 REMARK 620 2 HIS A 65 ND1 108.1 REMARK 620 3 HIS A 140 NE2 90.7 101.4 REMARK 620 4 ASP A 211 OD2 89.6 151.9 100.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 67 OD2 REMARK 620 2 HIS A 68 NE2 89.9 REMARK 620 3 ASP A 211 OD2 160.4 101.9 REMARK 620 4 HIS A 269 NE2 92.3 118.8 95.6 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 ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y44 RELATED DB: PDB REMARK 900 RELATED ID: 2FK6 RELATED DB: PDB DBREF 4GCW A 1 307 UNP P54548 RNZ_BACSU 1 307 DBREF 4GCW B 1 76 PDB 4GCW 4GCW 1 76 SEQADV 4GCW MET A 46 UNP P54548 ILE 46 ENGINEERED MUTATION SEQADV 4GCW MET A 228 UNP P54548 LEU 228 ENGINEERED MUTATION SEQADV 4GCW LYS A 308 UNP P54548 EXPRESSION TAG SEQADV 4GCW LEU A 309 UNP P54548 EXPRESSION TAG SEQADV 4GCW ALA A 310 UNP P54548 EXPRESSION TAG SEQADV 4GCW ALA A 311 UNP P54548 EXPRESSION TAG SEQADV 4GCW ALA A 312 UNP P54548 EXPRESSION TAG SEQADV 4GCW LEU A 313 UNP P54548 EXPRESSION TAG SEQADV 4GCW GLU A 314 UNP P54548 EXPRESSION TAG SEQADV 4GCW HIS A 315 UNP P54548 EXPRESSION TAG SEQADV 4GCW HIS A 316 UNP P54548 EXPRESSION TAG SEQADV 4GCW HIS A 317 UNP P54548 EXPRESSION TAG SEQADV 4GCW HIS A 318 UNP P54548 EXPRESSION TAG SEQADV 4GCW HIS A 319 UNP P54548 EXPRESSION TAG SEQADV 4GCW HIS A 320 UNP P54548 EXPRESSION TAG SEQRES 1 A 320 MET GLU LEU LEU PHE LEU GLY THR GLY ALA GLY ILE PRO SEQRES 2 A 320 ALA LYS ALA ARG ASN VAL THR SER VAL ALA LEU LYS LEU SEQRES 3 A 320 LEU GLU GLU ARG ARG SER VAL TRP LEU PHE ASP CYS GLY SEQRES 4 A 320 GLU ALA THR GLN HIS GLN MET LEU HIS THR THR ILE LYS SEQRES 5 A 320 PRO ARG LYS ILE GLU LYS ILE PHE ILE THR HIS MET HIS SEQRES 6 A 320 GLY ASP HIS VAL TYR GLY LEU PRO GLY LEU LEU GLY SER SEQRES 7 A 320 ARG SER PHE GLN GLY GLY GLU ASP GLU LEU THR VAL TYR SEQRES 8 A 320 GLY PRO LYS GLY ILE LYS ALA PHE ILE GLU THR SER LEU SEQRES 9 A 320 ALA VAL THR LYS THR HIS LEU THR TYR PRO LEU ALA ILE SEQRES 10 A 320 GLN GLU ILE GLU GLU GLY ILE VAL PHE GLU ASP ASP GLN SEQRES 11 A 320 PHE ILE VAL THR ALA VAL SER VAL ILE HIS GLY VAL GLU SEQRES 12 A 320 ALA PHE GLY TYR ARG VAL GLN GLU LYS ASP VAL PRO GLY SEQRES 13 A 320 SER LEU LYS ALA ASP VAL LEU LYS GLU MET ASN ILE PRO SEQRES 14 A 320 PRO GLY PRO VAL TYR GLN LYS ILE LYS LYS GLY GLU THR SEQRES 15 A 320 VAL THR LEU GLU ASP GLY ARG ILE ILE ASN GLY ASN ASP SEQRES 16 A 320 PHE LEU GLU PRO PRO LYS LYS GLY ARG SER VAL VAL PHE SEQRES 17 A 320 SER GLY ASP THR ARG VAL SER ASP LYS LEU LYS GLU LEU SEQRES 18 A 320 ALA ARG ASP CYS ASP VAL MET VAL HIS GLU ALA THR PHE SEQRES 19 A 320 ALA LYS GLU ASP ARG LYS LEU ALA TYR ASP TYR TYR HIS SEQRES 20 A 320 SER THR THR GLU GLN ALA ALA VAL THR ALA LYS GLU ALA SEQRES 21 A 320 ARG ALA LYS GLN LEU ILE LEU THR HIS ILE SER ALA ARG SEQRES 22 A 320 TYR GLN GLY ASP ALA SER LEU GLU LEU GLN LYS GLU ALA SEQRES 23 A 320 VAL ASP VAL PHE PRO ASN SER VAL ALA ALA TYR ASP PHE SEQRES 24 A 320 LEU GLU VAL ASN VAL PRO ARG GLY LYS LEU ALA ALA ALA SEQRES 25 A 320 LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 76 G C U U C C A U A G C U C SEQRES 2 B 76 A G C A G G U A G A G C A SEQRES 3 B 76 C U U C C A U G G U A A G SEQRES 4 B 76 G A A G A G G U C A G C G SEQRES 5 B 76 G U U C G A G C C C G C U SEQRES 6 B 76 U G G A A G C OMU OMU A2M A2M MODRES 4GCW OMU B 73 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 4GCW OMU B 74 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE HET OMU B 73 21 HET OMU B 74 21 HET ZN A 401 1 HET ZN A 402 1 HET MES A 403 12 HETNAM OMU O2'-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 2 OMU 2(C10 H15 N2 O9 P) FORMUL 3 ZN 2(ZN 2+) FORMUL 5 MES C6 H13 N O4 S FORMUL 6 HOH *32(H2 O) HELIX 1 1 LEU A 27 ARG A 31 1 5 HELIX 2 2 ALA A 41 LEU A 47 1 7 HELIX 3 3 LYS A 52 ARG A 54 5 3 HELIX 4 4 HIS A 65 TYR A 70 1 6 HELIX 5 5 GLY A 71 GLN A 82 1 12 HELIX 6 6 GLY A 95 VAL A 106 1 12 HELIX 7 7 LYS A 159 MET A 166 1 8 HELIX 8 8 PRO A 172 GLY A 180 1 9 HELIX 9 9 ASN A 192 LEU A 197 5 6 HELIX 10 10 SER A 215 ALA A 222 1 8 HELIX 11 11 ASP A 238 TYR A 245 1 8 HELIX 12 12 THR A 249 ARG A 261 1 13 HELIX 13 13 GLN A 275 ASP A 288 1 14 SHEET 1 A 7 LEU A 115 GLU A 119 0 SHEET 2 A 7 LEU A 88 GLY A 92 1 N VAL A 90 O ALA A 116 SHEET 3 A 7 ILE A 56 PHE A 60 1 N ILE A 59 O TYR A 91 SHEET 4 A 7 SER A 32 PHE A 36 1 N LEU A 35 O PHE A 60 SHEET 5 A 7 SER A 21 LEU A 26 -1 N LEU A 24 O TRP A 34 SHEET 6 A 7 GLU A 2 GLY A 7 -1 N LEU A 4 O ALA A 23 SHEET 7 A 7 GLU A 301 ASN A 303 -1 O VAL A 302 N LEU A 3 SHEET 1 B 7 GLY A 123 GLU A 127 0 SHEET 2 B 7 PHE A 131 VAL A 138 -1 O VAL A 133 N PHE A 126 SHEET 3 B 7 ALA A 144 GLU A 151 -1 O ALA A 144 N VAL A 138 SHEET 4 B 7 SER A 205 PHE A 208 -1 O VAL A 206 N VAL A 149 SHEET 5 B 7 VAL A 227 GLU A 231 1 O VAL A 229 N VAL A 207 SHEET 6 B 7 GLN A 264 THR A 268 1 O GLN A 264 N MET A 228 SHEET 7 B 7 SER A 293 ALA A 295 1 O VAL A 294 N LEU A 267 SHEET 1 C 2 VAL A 183 THR A 184 0 SHEET 2 C 2 ILE A 190 ILE A 191 -1 O ILE A 191 N VAL A 183 LINK O3' C B 72 P OMU B 73 1555 1555 1.63 LINK O3' OMU B 73 P OMU B 74 1555 1555 1.63 LINK NE2 HIS A 63 ZN ZN A 402 1555 1555 2.13 LINK ND1 HIS A 65 ZN ZN A 402 1555 1555 2.42 LINK OD2 ASP A 67 ZN ZN A 401 1555 1555 2.34 LINK NE2 HIS A 68 ZN ZN A 401 1555 1555 2.01 LINK NE2 HIS A 140 ZN ZN A 402 1555 1555 2.54 LINK OD2 ASP A 211 ZN ZN A 401 1555 1555 2.03 LINK OD2 ASP A 211 ZN ZN A 402 1555 1555 2.48 LINK NE2 HIS A 269 ZN ZN A 401 1555 1555 2.36 SITE 1 AC1 6 ASP A 67 HIS A 68 ASP A 211 HIS A 269 SITE 2 AC1 6 ZN A 402 OMU B 74 SITE 1 AC2 6 HIS A 63 HIS A 65 HIS A 140 ASP A 211 SITE 2 AC2 6 ZN A 401 OMU B 74 SITE 1 AC3 3 ARG A 54 ASP A 86 U B 4 CRYST1 174.080 42.550 110.890 90.00 127.18 90.00 C 1 2 1 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 0.005744 0.000000 0.004357 0.00000 SCALE2 0.000000 0.023502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011319 0.00000