HEADER OXIDOREDUCTASE 06-APR-12 4EJM TITLE CRYSTAL STRUCTURE OF A PUTATIVE ZINC-BINDING DEHYDROGENASE (TARGET TITLE 2 PSI-012003) FROM SINORHIZOBIUM MELILOTI 1021 BOUND TO NADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE ZINC-BINDING DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SHORT-CHAIN DEHYDROGENASE; COMPND 5 EC: 1.1.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SINORHIZOBIUM MELILOTI; SOURCE 3 ORGANISM_COMMON: ENSIFER MELILOTI; SOURCE 4 ORGANISM_TAXID: 266834; SOURCE 5 STRAIN: 1021; SOURCE 6 GENE: R01577, SMC01214; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSGC KEYWDS NADP, STRUCTURAL GENOMICS, NYSGRC, PSI-BIOLOGY, NEW YORK STRUCTURAL KEYWDS 2 GENOMICS RESEARCH CONSORTIUM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.SAMPATHKUMAR,S.C.ALMO,NEW YORK STRUCTURAL GENOMICS RESEARCH AUTHOR 2 CONSORTIUM (NYSGRC) REVDAT 2 15-NOV-17 4EJM 1 REMARK REVDAT 1 02-MAY-12 4EJM 0 JRNL AUTH P.SAMPATHKUMAR,N.BANU,R.BHOSLE,J.BONANNO,S.CHAMALA, JRNL AUTH 2 S.CHOWDHURY,A.FISER,A.GIZZI,A.S.GLENN,J.HAMMONDS, JRNL AUTH 3 B.HILLERICH,K.KHAFIZOV,J.D.LOVE,B.MATIKAINEN,Y.PATSKOVSKY, JRNL AUTH 4 R.SEIDEL,R.TORO,W.ZENCHECK,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE ZINC-BINDING DEHYDROGENASE JRNL TITL 2 (TARGET NYSGRC-012003) FROM SINORHIZOBIUM MELILOTI 1021 JRNL TITL 3 BOUND TO NADP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 24174 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1229 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) : 2.08 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.14 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1399 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.2460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2486 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -0.11000 REMARK 3 B33 (A**2) : 0.22000 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): 0.185 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.160 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.149 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2618 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1768 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3573 ; 1.546 ; 2.015 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4331 ; 0.937 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 351 ; 6.349 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;32.954 ;23.011 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 408 ;11.493 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;21.781 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 433 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2912 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 497 ; 0.001 ; 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 : MASK 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 4 REMARK 4 4EJM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071700. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24190 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11800 REMARK 200 FOR THE DATA SET : 22.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.91700 REMARK 200 FOR SHELL : 2.080 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: LIGAND STRUCTURE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN (20 MM HEPES, PH 7.5, 150 MM REMARK 280 NACL, 10% GLYCEROL; RESERVOIR (MCSG2 #1: 0.2 M POTASSIUM SODIUM REMARK 280 TARTARATE AND 20% (W/V) PEG3350 ); CRYOPROTECTION (30% ETHYLENE REMARK 280 GLYCOL); CRYSTALS SOAKED IN 100MM NADP AND 100MM 3- REMARK 280 HYDROXYBUTYRATE-NA IN 15% PEG3350 AND 30% ETHYLENEGLYCOL FOR AT REMARK 280 LEAST 30MINS, TEMPERATURE 298K, VAPOR DIFFUSION, SITTING DROP, REMARK 280 PH 6.2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 53.81000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 53.81000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 68.87050 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 53.81000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 53.81000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 68.87050 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 53.81000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 53.81000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 68.87050 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 53.81000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 53.81000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 68.87050 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 53.81000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 53.81000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 68.87050 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 53.81000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 53.81000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 68.87050 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 53.81000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 53.81000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 68.87050 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 53.81000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 53.81000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 68.87050 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A PROBABLE TETRAMER 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: 19160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 47130 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 107.62000 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 107.62000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 525 LIES ON A SPECIAL POSITION. 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 MSE A -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 SER A -15 REMARK 465 SER A -14 REMARK 465 GLY A -13 REMARK 465 VAL A -12 REMARK 465 ASP A -11 REMARK 465 LEU A -10 REMARK 465 GLY A -9 REMARK 465 THR A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 SER A 340 REMARK 465 ALA A 341 REMARK 465 GLU A 342 REMARK 465 ARG A 343 REMARK 465 VAL A 344 REMARK 465 ALA A 345 REMARK 465 GLN A 346 REMARK 465 GLN A 347 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 ARG A 72 CG CD NE CZ NH1 NH2 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 HIS A 293 CG HIS A 293 CD2 0.063 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 A 279 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 279 NE - CZ - NH2 ANGL. DEV. = -4.9 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 51 72.73 -116.10 REMARK 500 PRO A 76 136.58 -35.13 REMARK 500 ILE A 110 -57.41 -133.31 REMARK 500 GLU A 280 59.39 36.88 REMARK 500 ILE A 288 -136.96 42.89 REMARK 500 ALA A 330 -75.79 -40.76 REMARK 500 VAL A 333 -76.38 -107.12 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 91 SG REMARK 620 2 CYS A 102 SG 121.4 REMARK 620 3 CYS A 88 SG 109.9 102.5 REMARK 620 4 CYS A 94 SG 104.0 101.3 118.5 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 NAP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EJ6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A PUTATIVE L-THREONINE DEHYDROGENASE (TARGET REMARK 900 PSI-012003) FROM SINORHIZOBIUM MELILOTI 1021 REMARK 900 RELATED ID: NYSGRC-012003 RELATED DB: TARGETTRACK DBREF 4EJM A 1 347 UNP Q92PZ3 Q92PZ3_RHIME 1 347 SEQADV 4EJM MSE A -22 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM HIS A -21 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM HIS A -20 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM HIS A -19 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM HIS A -18 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM HIS A -17 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM HIS A -16 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM SER A -15 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM SER A -14 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM GLY A -13 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM VAL A -12 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM ASP A -11 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM LEU A -10 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM GLY A -9 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM THR A -8 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM GLU A -7 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM ASN A -6 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM LEU A -5 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM TYR A -4 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM PHE A -3 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM GLN A -2 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM SER A -1 UNP Q92PZ3 EXPRESSION TAG SEQADV 4EJM MSE A 0 UNP Q92PZ3 EXPRESSION TAG SEQRES 1 A 370 MSE HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 370 GLY THR GLU ASN LEU TYR PHE GLN SER MSE MSE LYS ALA SEQRES 3 A 370 VAL ARG LEU GLU SER VAL GLY ASN ILE SER VAL ARG ASN SEQRES 4 A 370 VAL GLY ILE PRO GLU PRO GLY PRO ASP ASP LEU LEU VAL SEQRES 5 A 370 LYS VAL GLU ALA CYS GLY ILE CYS GLY THR ASP ARG HIS SEQRES 6 A 370 LEU LEU HIS GLY GLU PHE PRO SER THR PRO PRO VAL THR SEQRES 7 A 370 LEU GLY HIS GLU PHE CYS GLY ILE VAL VAL GLU ALA GLY SEQRES 8 A 370 SER ALA VAL ARG ASP ILE ALA PRO GLY ALA ARG ILE THR SEQRES 9 A 370 GLY ASP PRO ASN ILE SER CYS GLY ARG CYS PRO GLN CYS SEQRES 10 A 370 GLN ALA GLY ARG VAL ASN LEU CYS ARG ASN LEU ARG ALA SEQRES 11 A 370 ILE GLY ILE HIS ARG ASP GLY GLY PHE ALA GLU TYR VAL SEQRES 12 A 370 LEU VAL PRO ARG LYS GLN ALA PHE GLU ILE PRO LEU THR SEQRES 13 A 370 LEU ASP PRO VAL HIS GLY ALA PHE CYS GLU PRO LEU ALA SEQRES 14 A 370 CYS CYS LEU HIS GLY VAL ASP LEU SER GLY ILE LYS ALA SEQRES 15 A 370 GLY SER THR VAL ALA ILE LEU GLY GLY GLY VAL ILE GLY SEQRES 16 A 370 LEU LEU THR VAL GLN LEU ALA ARG LEU ALA GLY ALA THR SEQRES 17 A 370 THR VAL ILE LEU SER THR ARG GLN ALA THR LYS ARG ARG SEQRES 18 A 370 LEU ALA GLU GLU VAL GLY ALA THR ALA THR VAL ASP PRO SEQRES 19 A 370 SER ALA GLY ASP VAL VAL GLU ALA ILE ALA GLY PRO VAL SEQRES 20 A 370 GLY LEU VAL PRO GLY GLY VAL ASP VAL VAL ILE GLU CYS SEQRES 21 A 370 ALA GLY VAL ALA GLU THR VAL LYS GLN SER THR ARG LEU SEQRES 22 A 370 ALA LYS ALA GLY GLY THR VAL VAL ILE LEU GLY VAL LEU SEQRES 23 A 370 PRO GLN GLY GLU LYS VAL GLU ILE GLU PRO PHE ASP ILE SEQRES 24 A 370 LEU PHE ARG GLU LEU ARG VAL LEU GLY SER PHE ILE ASN SEQRES 25 A 370 PRO PHE VAL HIS ARG ARG ALA ALA ASP LEU VAL ALA THR SEQRES 26 A 370 GLY ALA ILE GLU ILE ASP ARG MSE ILE SER ARG ARG ILE SEQRES 27 A 370 SER LEU ASP GLU ALA PRO ASP VAL ILE SER ASN PRO ALA SEQRES 28 A 370 ALA ALA GLY GLU VAL LYS VAL LEU VAL ILE PRO SER ALA SEQRES 29 A 370 GLU ARG VAL ALA GLN GLN MODRES 4EJM MSE A 0 MET SELENOMETHIONINE MODRES 4EJM MSE A 1 MET SELENOMETHIONINE MODRES 4EJM MSE A 310 MET SELENOMETHIONINE HET MSE A 0 8 HET MSE A 1 8 HET MSE A 310 8 HET ZN A 401 1 HET NAP A 402 48 HET EDO A 403 4 HET EDO A 404 4 HET EDO A 405 4 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 ZN ZN 2+ FORMUL 3 NAP C21 H28 N7 O17 P3 FORMUL 4 EDO 3(C2 H6 O2) FORMUL 7 HOH *110(H2 O) HELIX 1 1 CYS A 37 HIS A 45 1 9 HELIX 2 2 CYS A 91 ALA A 96 1 6 HELIX 3 3 ARG A 98 CYS A 102 5 5 HELIX 4 4 VAL A 137 ALA A 140 5 4 HELIX 5 5 PHE A 141 GLY A 156 1 16 HELIX 6 6 GLY A 169 ALA A 182 1 14 HELIX 7 7 GLN A 193 VAL A 203 1 11 HELIX 8 8 ASP A 215 GLY A 222 1 8 HELIX 9 9 VAL A 240 LEU A 250 1 11 HELIX 10 10 GLU A 272 ARG A 279 1 8 HELIX 11 11 VAL A 292 THR A 302 1 11 HELIX 12 12 ILE A 307 ARG A 309 5 3 HELIX 13 13 GLU A 319 ASN A 326 1 8 SHEET 1 A 3 ASN A 11 GLY A 18 0 SHEET 2 A 3 MSE A 0 SER A 8 -1 N SER A 8 O ASN A 11 SHEET 3 A 3 VAL A 54 THR A 55 -1 O VAL A 54 N LEU A 6 SHEET 1 B 5 TYR A 119 PRO A 123 0 SHEET 2 B 5 ASP A 26 ILE A 36 -1 N VAL A 29 O VAL A 120 SHEET 3 B 5 PHE A 60 ALA A 67 -1 O VAL A 65 N LEU A 28 SHEET 4 B 5 ARG A 79 GLY A 82 -1 O ILE A 80 N GLY A 62 SHEET 5 B 5 ALA A 127 ILE A 130 -1 O PHE A 128 N THR A 81 SHEET 1 C 4 TYR A 119 PRO A 123 0 SHEET 2 C 4 ASP A 26 ILE A 36 -1 N VAL A 29 O VAL A 120 SHEET 3 C 4 LYS A 334 VAL A 337 -1 O VAL A 337 N CYS A 34 SHEET 4 C 4 ILE A 311 ILE A 315 1 N ARG A 313 O LEU A 336 SHEET 1 D 2 ASN A 85 ILE A 86 0 SHEET 2 D 2 ARG A 106 ALA A 107 -1 O ARG A 106 N ILE A 86 SHEET 1 E 6 ALA A 207 VAL A 209 0 SHEET 2 E 6 THR A 186 SER A 190 1 N LEU A 189 O VAL A 209 SHEET 3 E 6 THR A 162 LEU A 166 1 N VAL A 163 O ILE A 188 SHEET 4 E 6 VAL A 231 GLU A 236 1 O ILE A 235 N ALA A 164 SHEET 5 E 6 ALA A 251 ILE A 259 1 O VAL A 258 N VAL A 234 SHEET 6 E 6 ARG A 282 GLY A 285 1 O ARG A 282 N VAL A 257 LINK C SER A -1 N MSE A 0 1555 1555 1.32 LINK C MSE A 0 N MSE A 1 1555 1555 1.34 LINK C MSE A 1 N LYS A 2 1555 1555 1.32 LINK C ARG A 309 N MSE A 310 1555 1555 1.34 LINK C MSE A 310 N ILE A 311 1555 1555 1.33 LINK SG CYS A 91 ZN ZN A 401 1555 1555 2.29 LINK SG CYS A 102 ZN ZN A 401 1555 1555 2.31 LINK SG CYS A 88 ZN ZN A 401 1555 1555 2.34 LINK SG CYS A 94 ZN ZN A 401 1555 1555 2.41 CISPEP 1 PRO A 52 PRO A 53 0 -4.36 SITE 1 AC1 4 CYS A 88 CYS A 91 CYS A 94 CYS A 102 SITE 1 AC2 25 CYS A 147 GLY A 167 GLY A 169 VAL A 170 SITE 2 AC2 25 ILE A 171 SER A 190 THR A 191 ARG A 192 SITE 3 AC2 25 GLN A 193 LYS A 196 CYS A 237 ALA A 238 SITE 4 AC2 25 GLU A 242 THR A 243 LEU A 260 GLY A 261 SITE 5 AC2 25 VAL A 262 SER A 286 ILE A 288 HOH A 504 SITE 6 AC2 25 HOH A 528 HOH A 546 HOH A 565 HOH A 582 SITE 7 AC2 25 HOH A 583 SITE 1 AC3 3 ARG A 197 ARG A 198 GLU A 201 SITE 1 AC4 5 HIS A 150 ASP A 153 PRO A 290 PHE A 291 SITE 2 AC4 5 VAL A 292 SITE 1 AC5 3 LEU A 101 ALA A 253 PHE A 278 CRYST1 107.620 107.620 137.741 90.00 90.00 90.00 I 4 2 2 16 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 0.009292 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009292 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007260 0.00000