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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
