HEADER OXIDOREDUCTASE 25-JAN-17 5ULV TITLE MALATE DEHYDROGENASE FROM METHYLOBACTERIUM EXTORQUENS 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 5 04-OCT-23 5ULV 1 LINK REVDAT 4 21-NOV-18 5ULV 1 JRNL REVDAT 3 14-NOV-18 5ULV 1 JRNL REVDAT 2 23-AUG-17 5ULV 1 SPRSDE REMARK REVDAT 1 08-FEB-17 5ULV 0 SPRSDE 23-AUG-17 5ULV 4ROR 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. 1.66 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 41822 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) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2191 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) : 1.66 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2872 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 176 REMARK 3 BIN FREE R VALUE : 0.2400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2323 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 354 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : -1.04000 REMARK 3 B12 (A**2) : 0.16000 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): 0.071 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.318 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2470 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2399 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3374 ; 1.909 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5540 ; 1.069 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 345 ; 5.817 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;36.427 ;25.213 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 409 ;13.047 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;23.546 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 395 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2880 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 510 ; 0.004 ; 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): 1323 ; 2.097 ; 2.004 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1322 ; 2.097 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1669 ; 3.055 ; 2.991 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1670 ; 3.055 ; 2.995 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1147 ; 2.919 ; 2.219 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1148 ; 2.918 ; 2.222 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1700 ; 4.518 ; 3.216 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3149 ; 6.688 ;17.321 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2908 ; 6.218 ;16.392 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 : NULL 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 5ULV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000226097. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-14 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 : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.127092 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44052 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 37.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 3GVH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25-28% PEG400, 180-220MM CACL2, 0.1M REMARK 280 HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, 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 34.88633 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 69.77267 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 34.88633 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 69.77267 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 34.88633 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 69.77267 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 34.88633 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 69.77267 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: 14790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -107.0 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 54.49750 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -94.39244 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 -34.88633 REMARK 350 BIOMT1 4 0.500000 0.866025 0.000000 54.49750 REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 -94.39244 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 -34.88633 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 818 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 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 ARG A 83 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 91 CG OD1 OD2 REMARK 470 GLU A 310 CG CD OE1 OE2 REMARK 470 ASP A 317 CG OD1 OD2 REMARK 470 LYS A 318 CG CD CE NZ 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 CA CA A 402 O HOH A 832 1.52 REMARK 500 OD1 ASP A 54 O HOH A 501 1.96 REMARK 500 ND2 ASN A 121 O HOH A 502 1.98 REMARK 500 NZ LYS A 207 O HOH A 503 2.16 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 574 O HOH A 574 10554 1.77 REMARK 500 O HOH A 541 O HOH A 541 9554 1.97 REMARK 500 O HOH A 600 O HOH A 600 10554 2.08 REMARK 500 O HOH A 541 O HOH A 799 9554 2.16 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 GLU A 166 CD GLU A 166 OE2 -0.072 REMARK 500 GLU A 206 CG GLU A 206 CD 0.098 REMARK 500 GLU A 206 CD GLU A 206 OE1 0.076 REMARK 500 GLU A 206 CD GLU A 206 OE2 0.100 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 34 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 152 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 152 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 PHE A 153 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 185 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 TYR A 186 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 252 NE - CZ - NH2 ANGL. DEV. = -3.7 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 ILE A 119 43.08 -141.94 REMARK 500 ALA A 145 -60.48 -150.98 REMARK 500 LYS A 227 -48.28 64.27 REMARK 500 PHE A 232 -26.46 -143.53 REMARK 500 ASP A 261 50.82 -102.36 REMARK 500 TYR A 264 18.47 56.53 REMARK 500 ASN A 316 116.74 -161.69 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 854 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 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 166 OE2 REMARK 620 2 GLU A 166 OE2 13.1 REMARK 620 3 HOH A 526 O 87.5 84.5 REMARK 620 4 HOH A 528 O 83.7 93.2 146.3 REMARK 620 5 HOH A 572 O 72.7 59.7 83.5 124.1 REMARK 620 6 HOH A 604 O 84.3 94.4 63.9 82.9 140.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 287 OE1 REMARK 620 2 GLU A 287 OE2 52.1 REMARK 620 3 GLU A 287 OE2 52.1 0.0 REMARK 620 4 HOH A 606 O 144.9 137.6 137.6 REMARK 620 5 HOH A 612 O 79.8 131.8 131.8 79.5 REMARK 620 6 HOH A 680 O 127.4 136.0 136.0 72.3 73.9 REMARK 620 7 HOH A 746 O 73.6 72.3 72.3 138.1 100.2 67.6 REMARK 620 8 HOH A 752 O 76.4 79.2 79.2 74.5 86.8 144.0 147.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA 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 DBREF 5ULV A 1 320 UNP B7KVX2 MDH_METC4 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 CA A 401 1 HET CA A 402 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) FORMUL 4 HOH *354(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 VAL A 31 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 77 SHEET 6 AA1 6 VAL A 141 GLY A 143 1 O VAL A 142 N VAL A 116 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 LEU A 269 N LEU A 260 SHEET 3 AA4 3 GLY A 281 VAL A 285 -1 O GLU A 283 N VAL A 276 LINK OE2AGLU A 166 CA CA A 402 1555 1555 2.71 LINK OE2BGLU A 166 CA CA A 402 1555 1555 3.05 LINK OE1 GLU A 287 CA CA A 401 1555 1555 2.49 LINK OE2 GLU A 287 CA CA A 401 1555 1555 2.52 LINK OE2 GLU A 287 CA CA A 401 1555 11655 2.28 LINK CA CA A 401 O HOH A 606 1555 11655 2.54 LINK CA CA A 401 O HOH A 612 1555 11655 2.39 LINK CA CA A 401 O HOH A 680 1555 11655 2.42 LINK CA CA A 401 O HOH A 746 1555 1555 2.57 LINK CA CA A 401 O HOH A 752 1555 1555 2.44 LINK CA CA A 402 O HOH A 526 1555 9554 2.48 LINK CA CA A 402 O HOH A 528 1555 1555 2.32 LINK CA CA A 402 O HOH A 572 1555 1555 2.06 LINK CA CA A 402 O HOH A 604 1555 9554 2.09 CISPEP 1 ASN A 121 PRO A 122 0 -3.00 SITE 1 AC1 6 GLU A 287 HOH A 606 HOH A 612 HOH A 680 SITE 2 AC1 6 HOH A 746 HOH A 752 SITE 1 AC2 6 GLU A 166 HOH A 526 HOH A 528 HOH A 572 SITE 2 AC2 6 HOH A 604 HOH A 832 CRYST1 108.995 108.995 104.659 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 0.009175 0.005297 0.000000 0.00000 SCALE2 0.000000 0.010594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009555 0.00000