HEADER OXIDOREDUCTASE 18-JAN-17 5UJK TITLE MALATE DEHYDROGENASE FROM METHYLOBACTERIUM EXTORQUENS, COMPLEXED WITH TITLE 2 NAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.37; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOBACTERIUM EXTORQUENS; SOURCE 3 ORGANISM_TAXID: 408; SOURCE 4 GENE: MDH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MALATE, DEHYDROGENASE, NAD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.GONZALEZ REVDAT 4 04-OCT-23 5UJK 1 LINK REVDAT 3 21-NOV-18 5UJK 1 JRNL REVDAT 2 14-NOV-18 5UJK 1 JRNL REVDAT 1 08-FEB-17 5UJK 0 JRNL AUTH J.M.GONZALEZ,R.MARTI-ARBONA,J.C.H.CHEN,B.BROOM-PELTZ, JRNL AUTH 2 C.J.UNKEFER JRNL TITL CONFORMATIONAL CHANGES ON SUBSTRATE BINDING REVEALED BY JRNL TITL 2 STRUCTURES OF METHYLOBACTERIUM EXTORQUENS MALATE JRNL TITL 3 DEHYDROGENASE. JRNL REF ACTA CRYSTALLOGR F STRUCT V. 74 610 2018 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 2053-230X JRNL PMID 30279311 JRNL DOI 10.1107/S2053230X18011809 REMARK 2 REMARK 2 RESOLUTION. 1.53 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 51855 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) : 0.126 REMARK 3 R VALUE (WORKING SET) : 0.124 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2774 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) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3766 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE SET COUNT : 195 REMARK 3 BIN FREE R VALUE : 0.2750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2294 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 292 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41000 REMARK 3 B22 (A**2) : 0.41000 REMARK 3 B33 (A**2) : -1.33000 REMARK 3 B12 (A**2) : 0.20000 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): 0.058 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.063 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.392 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2428 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2314 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3313 ; 1.791 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5327 ; 1.033 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 326 ; 5.615 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;40.203 ;24.891 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 379 ;11.789 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;17.400 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 386 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2786 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 510 ; 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): 1280 ; 2.805 ;25.792 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1279 ; 2.806 ;25.808 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1605 ; 3.323 ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1606 ; 3.322 ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1148 ; 4.439 ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1149 ; 4.443 ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1706 ; 5.076 ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3011 ; 5.046 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2848 ; 4.722 ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2235 ; 4.333 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 5 ;16.634 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2241 ;14.779 ; 5.000 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 3 POSITIONS REMARK 4 REMARK 4 5UJK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000225974. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54696 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 54.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.00 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 4ROP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25-28% PEG400, 180-220MM CACL2, 0.1M REMARK 280 HEPES PH 7.5, SOAKED WITH 1MM NAD, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 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 REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 34.77367 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 69.54733 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 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 34.77367 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 69.54733 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 34.77367 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 69.54733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.77367 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 69.54733 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: 20410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -171.0 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 54.09450 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -93.69442 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 -34.77367 REMARK 350 BIOMT1 4 0.500000 0.866025 0.000000 54.09450 REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 -93.69442 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 -34.77367 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 669 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 758 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 MET A 1 REMARK 465 ASP A 317 REMARK 465 LYS A 318 REMARK 465 LEU A 319 REMARK 465 ALA A 320 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 LYS A 84 CG CD CE NZ REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 LYS A 295 CG CD CE NZ REMARK 470 GLU A 299 CG CD OE1 OE2 REMARK 470 LYS A 300 CG CD CE NZ REMARK 470 LEU A 308 CG CD1 CD2 REMARK 470 GLU A 310 CG CD OE1 OE2 REMARK 470 SER A 314 OG REMARK 470 VAL A 315 CG1 CG2 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 A 279 O HOH A 501 2.12 REMARK 500 O HOH A 524 O HOH A 733 2.15 REMARK 500 OD2 ASP A 124 O HOH A 502 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 545 O HOH A 545 10554 1.67 REMARK 500 O HOH A 654 O HOH A 654 12544 1.74 REMARK 500 O HOH A 593 O HOH A 593 10554 2.01 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 150 CB SER A 150 OG -0.078 REMARK 500 GLU A 206 CG GLU A 206 CD 0.114 REMARK 500 GLU A 206 CD GLU A 206 OE1 0.080 REMARK 500 GLU A 206 CD GLU A 206 OE2 0.073 REMARK 500 GLU A 279 CD GLU A 279 OE2 -0.071 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 ASP A 54 CB - CG - OD2 ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG A 252 NE - CZ - NH2 ANGL. DEV. = -3.6 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 PRO A 85 -33.24 -37.09 REMARK 500 ALA A 145 -56.50 -155.95 REMARK 500 LYS A 227 -34.83 64.07 REMARK 500 ASP A 261 41.71 -107.54 REMARK 500 TYR A 264 18.95 58.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 792 DISTANCE = 5.85 ANGSTROMS 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 A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 166 OE2 REMARK 620 2 HOH A 510 O 86.9 REMARK 620 3 HOH A 607 O 92.6 65.6 REMARK 620 4 HOH A 646 O 69.2 85.6 147.1 REMARK 620 5 HOH A 663 O 88.7 146.3 81.3 123.6 REMARK 620 6 HOH A 728 O 125.8 122.5 139.4 69.3 86.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 287 OE1 REMARK 620 2 GLU A 287 OE2 51.9 REMARK 620 3 GLU A 287 OE2 51.9 0.0 REMARK 620 4 HOH A 612 O 79.2 130.9 130.9 REMARK 620 5 HOH A 614 O 145.9 138.6 138.6 79.5 REMARK 620 6 HOH A 673 O 124.8 134.0 134.0 74.8 74.0 REMARK 620 7 HOH A 705 O 72.4 70.9 70.9 101.2 138.2 66.3 REMARK 620 8 HOH A 714 O 75.7 79.7 79.7 84.7 76.0 146.1 145.7 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 510 O REMARK 620 2 HOH A 607 O 49.5 REMARK 620 3 HOH A 646 O 63.0 88.4 REMARK 620 4 HOH A 663 O 99.6 59.6 84.0 REMARK 620 5 HOH A 728 O 126.9 142.2 66.1 89.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 404 DBREF 5UJK A 1 320 UNP A9W386 MDH_METEP 1 320 SEQRES 1 A 320 MET ALA ARG SER LYS ILE ALA LEU ILE GLY ALA GLY GLN SEQRES 2 A 320 ILE GLY GLY THR LEU ALA HIS LEU ALA GLY LEU LYS GLU SEQRES 3 A 320 LEU GLY ASP VAL VAL LEU PHE ASP ILE VAL ASP GLY VAL SEQRES 4 A 320 PRO GLN GLY LYS ALA LEU ASP ILE ALA GLU SER ALA PRO SEQRES 5 A 320 VAL ASP GLY PHE ASP ALA LYS TYR SER GLY ALA SER ASP SEQRES 6 A 320 TYR SER ALA ILE ALA GLY ALA ASP VAL VAL ILE VAL THR SEQRES 7 A 320 ALA GLY VAL PRO ARG LYS PRO GLY MET SER ARG ASP ASP SEQRES 8 A 320 LEU ILE GLY ILE ASN LEU LYS VAL MET GLU ALA VAL GLY SEQRES 9 A 320 ALA GLY ILE LYS GLU HIS ALA PRO ASP ALA PHE VAL ILE SEQRES 10 A 320 CYS ILE THR ASN PRO LEU ASP ALA MET VAL TRP ALA LEU SEQRES 11 A 320 GLN LYS PHE SER GLY LEU PRO THR ASN LYS VAL VAL GLY SEQRES 12 A 320 MET ALA GLY VAL LEU ASP SER ALA ARG PHE ARG HIS PHE SEQRES 13 A 320 LEU ALA GLU GLU PHE GLY VAL SER VAL GLU ASP VAL THR SEQRES 14 A 320 ALA PHE VAL LEU GLY GLY HIS GLY ASP ASP MET VAL PRO SEQRES 15 A 320 LEU THR ARG TYR SER THR VAL ALA GLY VAL PRO LEU THR SEQRES 16 A 320 ASP LEU VAL LYS LEU GLY TRP THR THR GLN GLU LYS LEU SEQRES 17 A 320 ASP ALA MET VAL GLU ARG THR ARG LYS GLY GLY GLY GLU SEQRES 18 A 320 ILE VAL ASN LEU LEU LYS THR GLY SER ALA PHE TYR ALA SEQRES 19 A 320 PRO ALA ALA SER ALA ILE ALA MET ALA GLU SER TYR LEU SEQRES 20 A 320 ARG ASP LYS LYS ARG VAL LEU PRO CYS ALA ALA TYR LEU SEQRES 21 A 320 ASP GLY GLN TYR GLY ILE ASP GLY LEU TYR VAL GLY VAL SEQRES 22 A 320 PRO VAL VAL ILE GLY GLU ASN GLY VAL GLU ARG VAL LEU SEQRES 23 A 320 GLU VAL THR PHE ASN ASP ASP GLU LYS ALA MET PHE GLU SEQRES 24 A 320 LYS SER VAL ASN SER VAL LYS GLY LEU ILE GLU ALA CYS SEQRES 25 A 320 LYS SER VAL ASN ASP LYS LEU ALA HET NAD A 401 44 HET CA A 402 1 HET CA A 403 2 HET CL A 404 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 CA 2(CA 2+) FORMUL 5 CL CL 1- FORMUL 6 HOH *292(H2 O) HELIX 1 AA1 GLY A 12 LYS A 25 1 14 HELIX 2 AA2 GLY A 38 GLY A 55 1 18 HELIX 3 AA3 ASP A 65 ALA A 70 5 6 HELIX 4 AA4 SER A 88 ALA A 111 1 24 HELIX 5 AA5 PRO A 122 GLY A 135 1 14 HELIX 6 AA6 PRO A 137 ASN A 139 5 3 HELIX 7 AA7 ALA A 145 GLY A 162 1 18 HELIX 8 AA8 SER A 164 GLU A 166 5 3 HELIX 9 AA9 HIS A 176 ASP A 178 5 3 HELIX 10 AB1 THR A 184 TYR A 186 5 3 HELIX 11 AB2 LEU A 194 LEU A 200 1 7 HELIX 12 AB3 THR A 204 LYS A 217 1 14 HELIX 13 AB4 LYS A 217 LYS A 227 1 11 HELIX 14 AB5 PHE A 232 ARG A 248 1 17 HELIX 15 AB6 GLN A 263 GLY A 265 5 3 HELIX 16 AB7 ASN A 291 VAL A 315 1 25 SHEET 1 AA1 6 TYR A 60 ALA A 63 0 SHEET 2 AA1 6 ASP A 29 PHE A 33 1 N LEU A 32 O SER A 61 SHEET 3 AA1 6 LYS A 5 ILE A 9 1 N LEU A 8 O PHE A 33 SHEET 4 AA1 6 VAL A 74 VAL A 77 1 O VAL A 74 N ALA A 7 SHEET 5 AA1 6 PHE A 115 CYS A 118 1 O ILE A 117 N VAL A 75 SHEET 6 AA1 6 VAL A 141 GLY A 143 1 O VAL A 142 N CYS A 118 SHEET 1 AA2 3 VAL A 168 THR A 169 0 SHEET 2 AA2 3 THR A 188 VAL A 189 -1 O THR A 188 N THR A 169 SHEET 3 AA2 3 VAL A 192 PRO A 193 -1 O VAL A 192 N VAL A 189 SHEET 1 AA3 2 VAL A 172 GLY A 174 0 SHEET 2 AA3 2 MET A 180 PRO A 182 -1 O VAL A 181 N LEU A 173 SHEET 1 AA4 3 ARG A 252 ASP A 261 0 SHEET 2 AA4 3 ASP A 267 GLY A 278 -1 O VAL A 275 N LEU A 254 SHEET 3 AA4 3 GLY A 281 VAL A 285 -1 O GLU A 283 N VAL A 276 LINK OE2 GLU A 166 CA A CA A 403 1555 1555 2.84 LINK OE1 GLU A 287 CA CA A 402 1555 1555 2.50 LINK OE2 GLU A 287 CA CA A 402 1555 1555 2.56 LINK OE2 GLU A 287 CA CA A 402 1555 11655 2.29 LINK CA CA A 402 O HOH A 612 1555 11655 2.40 LINK CA CA A 402 O HOH A 614 1555 11655 2.51 LINK CA CA A 402 O HOH A 673 1555 11655 2.51 LINK CA CA A 402 O HOH A 705 1555 1555 2.54 LINK CA CA A 402 O HOH A 714 1555 1555 2.39 LINK CA A CA A 403 O HOH A 510 1555 9554 2.55 LINK CA B CA A 403 O HOH A 510 1555 9554 3.17 LINK CA A CA A 403 O HOH A 607 1555 9554 1.95 LINK CA B CA A 403 O HOH A 607 1555 9554 2.68 LINK CA A CA A 403 O HOH A 646 1555 12544 2.08 LINK CA B CA A 403 O HOH A 646 1555 12544 2.87 LINK CA A CA A 403 O HOH A 663 1555 1555 2.22 LINK CA B CA A 403 O HOH A 663 1555 1555 2.80 LINK CA A CA A 403 O HOH A 728 1555 4545 2.62 LINK CA B CA A 403 O HOH A 728 1555 4545 1.86 CISPEP 1 ASN A 121 PRO A 122 0 -5.59 SITE 1 AC1 31 GLY A 12 GLN A 13 ILE A 14 PHE A 33 SITE 2 AC1 31 ASP A 34 ILE A 35 VAL A 36 THR A 78 SITE 3 AC1 31 ALA A 79 GLY A 80 VAL A 99 ILE A 119 SITE 4 AC1 31 ASN A 121 MET A 144 LEU A 148 HIS A 176 SITE 5 AC1 31 HOH A 512 HOH A 517 HOH A 522 HOH A 528 SITE 6 AC1 31 HOH A 546 HOH A 549 HOH A 559 HOH A 579 SITE 7 AC1 31 HOH A 580 HOH A 595 HOH A 635 HOH A 642 SITE 8 AC1 31 HOH A 658 HOH A 712 HOH A 726 SITE 1 AC2 6 GLU A 287 HOH A 612 HOH A 614 HOH A 673 SITE 2 AC2 6 HOH A 705 HOH A 714 SITE 1 AC3 6 GLU A 166 HOH A 510 HOH A 607 HOH A 646 SITE 2 AC3 6 HOH A 663 HOH A 728 SITE 1 AC4 4 ARG A 154 ARG A 252 HOH A 574 HOH A 727 CRYST1 108.189 108.189 104.321 90.00 90.00 120.00 P 64 2 2 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 0.009243 0.005336 0.000000 0.00000 SCALE2 0.000000 0.010673 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009586 0.00000