HEADER HYDROLASE 27-JAN-05 1YOE TITLE CRYSTAL STRUCTURE OF A THE E. COLI PYRIMIDINE NUCLEOSIDE HYDROLASE TITLE 2 YBEK WITH BOUND RIBOSE CAVEAT 1YOE RIB A 2001 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN YBEK; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.8; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: YBEK/RIHA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: WK6; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS PYRIMIDINE NUCLEOSIDE HYDROLASE, BACTERIAL NUCLEOSIDASE, RIBOSE, KEYWDS 2 ENZYME-PRODUCT COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.MUZZOLINI,W.VERSEES,J.STEYAERT,M.DEGANO REVDAT 5 25-OCT-23 1YOE 1 HETSYN REVDAT 4 29-JUL-20 1YOE 1 CAVEAT COMPND REMARK SEQADV REVDAT 4 2 1 HETNAM LINK SITE ATOM REVDAT 3 13-JUL-11 1YOE 1 VERSN REVDAT 2 24-FEB-09 1YOE 1 VERSN REVDAT 1 17-JAN-06 1YOE 0 JRNL AUTH L.MUZZOLINI,W.VERSEES,J.STEYAERT,M.DEGANO JRNL TITL CRYSTAL STRUCTURE OF THE E. COLI PYRIMIDINE NUCLEOSIDE JRNL TITL 2 HYDROLASE YBEK WITH BOUND RIBOSE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.GIABBAI,M.DEGANO REMARK 1 TITL CRYSTAL STRUCTURE TO 1.7 A OF THE ESCHERICHIA COLI REMARK 1 TITL 2 PYRIMIDINE NUCLEOSIDE HYDROLASE YEIK, A NOVEL CANDIDATE FOR REMARK 1 TITL 3 CANCER GENE THERAPY REMARK 1 REF STRUCTURE V. 12 739 2004 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 15130467 REMARK 1 DOI 10.1016/J.STR.2004.03.018 REMARK 1 REFERENCE 2 REMARK 1 AUTH W.VERSEES,K.DECANNIERE,R.PELLE,J.DEPOORTER,E.BROSENS, REMARK 1 AUTH 2 D.W.PARKIN,J.STEYAERT REMARK 1 TITL STRUCTURE AND FUNCTION OF A NOVEL PURINE SPECIFIC NUCLEOSIDE REMARK 1 TITL 2 HYDROLASE FROM TRYPANOSOMA VIVAX REMARK 1 REF J.MOL.BIOL. V. 307 1363 2001 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 11292348 REMARK 1 DOI 10.1006/JMBI.2001.4548 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.DEGANO,S.C.ALMO,J.C.SACCHETTINI,V.L.SCHRAMM REMARK 1 TITL TRYPANOSOMAL NUCLEOSIDE HYDROLASE. A NOVEL MECHANISM FROM REMARK 1 TITL 2 THE STRUCTURE WITH A TRANSITION-STATE INHIBITOR REMARK 1 REF BIOCHEMISTRY V. 37 6277 1998 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 9572842 REMARK 1 DOI 10.1021/BI973012E REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.19 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) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 34056 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1086 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) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1826 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2295 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 215 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 18.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.62000 REMARK 3 B22 (A**2) : -0.79000 REMARK 3 B33 (A**2) : 0.17000 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): 0.102 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.818 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2399 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3278 ; 1.305 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 301 ; 5.275 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 388 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1780 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1123 ; 0.191 ; 0.200 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): 165 ; 0.093 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.060 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 60 ; 0.180 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 38 ; 0.131 ; 0.200 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): 1516 ; 1.000 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2467 ; 1.743 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 883 ; 2.862 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 811 ; 4.618 ;10.000 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 : 1 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 1 A 311 REMARK 3 ORIGIN FOR THE GROUP (A): -4.4330 20.7639 36.7434 REMARK 3 T TENSOR REMARK 3 T11: 0.0052 T22: 0.0178 REMARK 3 T33: 0.0061 T12: -0.0005 REMARK 3 T13: -0.0056 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.1453 L22: 0.3512 REMARK 3 L33: 0.1442 L12: 0.0651 REMARK 3 L13: 0.0439 L23: 0.0581 REMARK 3 S TENSOR REMARK 3 S11: -0.0032 S12: 0.0185 S13: 0.0038 REMARK 3 S21: -0.0295 S22: 0.0249 S23: 0.0211 REMARK 3 S31: -0.0068 S32: 0.0061 S33: -0.0217 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: NULL REMARK 4 REMARK 4 1YOE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34056 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11600 REMARK 200 FOR THE DATA SET : 26.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.47500 REMARK 200 FOR SHELL : 2.900 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: YEIK PDB CODE 1Q8F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SODIUM ACETATE, RIBOSE, PH 5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 38.23300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.03100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 56.24150 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.23300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.03100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.24150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.23300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 42.03100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.24150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.23300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 42.03100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 56.24150 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 112.48300 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 112.48300 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -118.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 112.48300 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 112.48300 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 84.06200 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 112.48300 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 84.06200 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 112.48300 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 -10 REMARK 465 ARG A -9 REMARK 465 GLY A -8 REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 ASP A 79 REMARK 465 ASN A 80 REMARK 465 VAL A 81 REMARK 465 HIS A 82 REMARK 465 GLY A 83 REMARK 465 TYR A 226 REMARK 465 HIS A 227 REMARK 465 LYS A 228 REMARK 465 ASP A 229 REMARK 465 GLU A 230 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 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD1 REMARK 620 2 ASP A 15 OD1 82.0 REMARK 620 3 ASP A 15 OD2 71.2 51.9 REMARK 620 4 THR A 124 O 91.9 137.6 86.3 REMARK 620 5 ASP A 241 OD2 141.7 74.3 70.5 86.1 REMARK 620 6 RIB A2001 O2 120.8 82.4 132.2 134.0 85.7 REMARK 620 7 RIB A2001 O2 123.2 75.6 124.3 137.8 79.5 8.2 REMARK 620 8 RIB A2001 O3 136.6 133.7 146.6 76.3 79.9 57.6 62.2 REMARK 620 9 RIB A2001 O3 140.0 133.2 141.7 73.8 75.7 60.3 64.3 4.9 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MAS RELATED DB: PDB REMARK 900 RELATED ID: 2MAS RELATED DB: PDB REMARK 900 RELATED ID: 1EZR RELATED DB: PDB REMARK 900 RELATED ID: 1Q8F RELATED DB: PDB REMARK 900 RELATED ID: 1HOZ RELATED DB: PDB REMARK 900 RELATED ID: 1KIE RELATED DB: PDB DBREF 1YOE A 2 311 UNP P41409 YBEK_ECOLI 2 311 SEQADV 1YOE MET A -10 UNP P41409 EXPRESSION TAG SEQADV 1YOE ARG A -9 UNP P41409 EXPRESSION TAG SEQADV 1YOE GLY A -8 UNP P41409 EXPRESSION TAG SEQADV 1YOE SER A -7 UNP P41409 EXPRESSION TAG SEQADV 1YOE HIS A -6 UNP P41409 EXPRESSION TAG SEQADV 1YOE HIS A -5 UNP P41409 EXPRESSION TAG SEQADV 1YOE HIS A -4 UNP P41409 EXPRESSION TAG SEQADV 1YOE HIS A -3 UNP P41409 EXPRESSION TAG SEQADV 1YOE HIS A -2 UNP P41409 EXPRESSION TAG SEQADV 1YOE HIS A -1 UNP P41409 EXPRESSION TAG SEQADV 1YOE GLY A 0 UNP P41409 EXPRESSION TAG SEQADV 1YOE SER A 1 UNP P41409 EXPRESSION TAG SEQRES 1 A 322 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ALA SEQRES 2 A 322 LEU PRO ILE LEU LEU ASP CYS ASP PRO GLY HIS ASP ASP SEQRES 3 A 322 ALA ILE ALA ILE VAL LEU ALA LEU ALA SER PRO GLU LEU SEQRES 4 A 322 ASP VAL LYS ALA ILE THR SER SER ALA GLY ASN GLN THR SEQRES 5 A 322 PRO GLU LYS THR LEU ARG ASN VAL LEU ARG MET LEU THR SEQRES 6 A 322 LEU LEU ASN ARG THR ASP ILE PRO VAL ALA GLY GLY ALA SEQRES 7 A 322 VAL LYS PRO LEU MET ARG GLU LEU ILE ILE ALA ASP ASN SEQRES 8 A 322 VAL HIS GLY GLU SER GLY LEU ASP GLY PRO ALA LEU PRO SEQRES 9 A 322 GLU PRO THR PHE ALA PRO GLN ASN CYS THR ALA VAL GLU SEQRES 10 A 322 LEU MET ALA LYS THR LEU ARG GLU SER ALA GLU PRO VAL SEQRES 11 A 322 THR ILE VAL SER THR GLY PRO GLN THR ASN VAL ALA LEU SEQRES 12 A 322 LEU LEU ASN SER HIS PRO GLU LEU HIS SER LYS ILE ALA SEQRES 13 A 322 ARG ILE VAL ILE MET GLY GLY ALA MET GLY LEU GLY ASN SEQRES 14 A 322 TRP THR PRO ALA ALA GLU PHE ASN ILE TYR VAL ASP PRO SEQRES 15 A 322 GLU ALA ALA GLU ILE VAL PHE GLN SER GLY ILE PRO VAL SEQRES 16 A 322 VAL MET ALA GLY LEU ASP VAL THR HIS LYS ALA GLN ILE SEQRES 17 A 322 HIS VAL GLU ASP THR GLU ARG PHE ARG ALA ILE GLY ASN SEQRES 18 A 322 PRO VAL SER THR ILE VAL ALA GLU LEU LEU ASP PHE PHE SEQRES 19 A 322 LEU GLU TYR HIS LYS ASP GLU LYS TRP GLY PHE VAL GLY SEQRES 20 A 322 ALA PRO LEU HIS ASP PRO CYS THR ILE ALA TRP LEU LEU SEQRES 21 A 322 LYS PRO GLU LEU PHE THR SER VAL GLU ARG TRP VAL GLY SEQRES 22 A 322 VAL GLU THR GLN GLY LYS TYR THR GLN GLY MET THR VAL SEQRES 23 A 322 VAL ASP TYR TYR TYR LEU THR GLY ASN LYS PRO ASN ALA SEQRES 24 A 322 THR VAL MET VAL ASP VAL ASP ARG GLN GLY PHE VAL ASP SEQRES 25 A 322 LEU LEU ALA ASP ARG LEU LYS PHE TYR ALA HET RIB A2001 20 HET CA A1001 1 HETNAM RIB ALPHA-D-RIBOFURANOSE HETNAM CA CALCIUM ION HETSYN RIB ALPHA-D-RIBOSE; D-RIBOSE; RIBOSE FORMUL 2 RIB C5 H10 O5 FORMUL 3 CA CA 2+ FORMUL 4 HOH *215(H2 O) HELIX 1 1 GLY A 12 ALA A 24 1 13 HELIX 2 2 THR A 41 LEU A 56 1 16 HELIX 3 3 THR A 103 SER A 115 1 13 HELIX 4 4 GLN A 127 HIS A 137 1 11 HELIX 5 5 PRO A 138 SER A 142 5 5 HELIX 6 6 GLU A 164 ASP A 170 1 7 HELIX 7 7 ASP A 170 GLN A 179 1 10 HELIX 8 8 GLY A 188 HIS A 193 1 6 HELIX 9 9 HIS A 198 GLY A 209 1 12 HELIX 10 10 ASN A 210 GLU A 225 1 16 HELIX 11 11 ASP A 241 LYS A 250 1 10 HELIX 12 12 ASP A 295 LYS A 308 1 14 HELIX 13 13 PHE A 309 ALA A 311 5 3 SHEET 1 A 8 VAL A 63 GLY A 65 0 SHEET 2 A 8 LEU A 28 SER A 35 1 N SER A 35 O ALA A 64 SHEET 3 A 8 LEU A 3 CYS A 9 1 N ILE A 5 O LYS A 31 SHEET 4 A 8 VAL A 119 SER A 123 1 O VAL A 122 N LEU A 6 SHEET 5 A 8 ILE A 144 MET A 150 1 O VAL A 148 N ILE A 121 SHEET 6 A 8 VAL A 184 ALA A 187 1 O VAL A 185 N ILE A 149 SHEET 7 A 8 ALA A 288 VAL A 294 1 O THR A 289 N MET A 186 SHEET 8 A 8 PHE A 254 ARG A 259 -1 N VAL A 257 O VAL A 290 SHEET 1 B 2 GLN A 196 ILE A 197 0 SHEET 2 B 2 ALA A 237 PRO A 238 -1 O ALA A 237 N ILE A 197 SHEET 1 C 2 VAL A 261 VAL A 263 0 SHEET 2 C 2 THR A 274 VAL A 276 -1 O VAL A 275 N GLY A 262 LINK OD1 ASP A 10 CA CA A1001 1555 1555 2.46 LINK OD1 ASP A 15 CA CA A1001 1555 1555 2.48 LINK OD2 ASP A 15 CA CA A1001 1555 1555 2.49 LINK O THR A 124 CA CA A1001 1555 1555 2.36 LINK OD2 ASP A 241 CA CA A1001 1555 1555 2.42 LINK CA CA A1001 O2 ARIB A2001 1555 1555 2.73 LINK CA CA A1001 O2 BRIB A2001 1555 1555 2.44 LINK CA CA A1001 O3 ARIB A2001 1555 1555 2.70 LINK CA CA A1001 O3 BRIB A2001 1555 1555 2.61 LINK CA CA A1001 O HOH A2002 1555 1555 2.52 CISPEP 1 PRO A 11 GLY A 12 0 -10.94 CRYST1 76.466 84.062 112.483 90.00 90.00 90.00 I 2 2 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 0.013078 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011896 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008890 0.00000