HEADER OXIDOREDUCTASE 05-FEB-24 8RWL TITLE CRYSTAL STRUCTURE OF METHANOPYRUS KANDLERI MALATE DEHYDROGENASE MUTANT TITLE 2 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALATE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.1.1.299; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOPYRUS KANDLERI; SOURCE 3 ORGANISM_TAXID: 2320; SOURCE 4 GENE: MDH, MK1069; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MALATE DEHYDROGENASE, ROSSMANN-LIKE MOTIF, NAD(P)H BINDING SITE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.COQUILLE,J.ROCHE,S.ENGILBERGE,E.GIRARD,D.MADERN REVDAT 1 10-JUL-24 8RWL 0 JRNL AUTH S.COQUILLE,C.SIMOES PEREIRA,C.BROCHIER-ARMANET,J.ROCHE, JRNL AUTH 2 G.SANTONI,N.COQUELLE,E.GIRARD,F.STERPONE,D.MADERN JRNL TITL NAVIGATING THE CONFORMATIONAL LANDSCAPE OF AN ENZYME. JRNL TITL 2 STABILIZATION OF A LOW POPULATED CONFORMER BY EVOLUTIONARY JRNL TITL 3 MUTATIONS TRIGGERS ALLOSTERY INTO A NON-ALLOSTERIC ENZYME. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21_5207 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 35653 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1782 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.9200 - 5.3800 1.00 2842 150 0.2194 0.2427 REMARK 3 2 5.3700 - 4.2800 1.00 2687 142 0.1720 0.2134 REMARK 3 3 4.2800 - 3.7400 1.00 2628 138 0.1782 0.2082 REMARK 3 4 3.7400 - 3.4000 1.00 2620 138 0.1976 0.2444 REMARK 3 5 3.4000 - 3.1600 1.00 2612 137 0.2091 0.2548 REMARK 3 6 3.1600 - 2.9700 1.00 2595 137 0.2131 0.2626 REMARK 3 7 2.9700 - 2.8300 1.00 2577 135 0.2338 0.2569 REMARK 3 8 2.8300 - 2.7000 1.00 2564 135 0.2179 0.2771 REMARK 3 9 2.7000 - 2.6000 1.00 2575 136 0.2163 0.2754 REMARK 3 10 2.6000 - 2.5100 1.00 2556 135 0.2287 0.2944 REMARK 3 11 2.5100 - 2.4300 1.00 2544 134 0.2467 0.3282 REMARK 3 12 2.4300 - 2.3600 1.00 2556 134 0.2585 0.2845 REMARK 3 13 2.3600 - 2.3000 0.99 2515 131 0.2832 0.3078 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.262 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.095 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 4678 REMARK 3 ANGLE : 0.998 6355 REMARK 3 CHIRALITY : 0.054 783 REMARK 3 PLANARITY : 0.007 806 REMARK 3 DIHEDRAL : 16.327 1711 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 146 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.8220 -3.0220 -22.5595 REMARK 3 T TENSOR REMARK 3 T11: 0.4297 T22: 0.7356 REMARK 3 T33: 0.4456 T12: -0.1857 REMARK 3 T13: -0.0835 T23: 0.1372 REMARK 3 L TENSOR REMARK 3 L11: 6.4823 L22: 2.3671 REMARK 3 L33: 2.9887 L12: -1.2351 REMARK 3 L13: -1.4227 L23: -0.0581 REMARK 3 S TENSOR REMARK 3 S11: -0.0968 S12: 0.7949 S13: 0.4626 REMARK 3 S21: -0.1982 S22: -0.0972 S23: -0.2568 REMARK 3 S31: -0.5281 S32: 0.6303 S33: 0.1495 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 147 THROUGH 224 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.0108 -30.8329 -17.4384 REMARK 3 T TENSOR REMARK 3 T11: 0.4510 T22: 0.6720 REMARK 3 T33: 0.5485 T12: 0.1111 REMARK 3 T13: 0.0219 T23: -0.0782 REMARK 3 L TENSOR REMARK 3 L11: 4.9244 L22: 3.0506 REMARK 3 L33: 5.6399 L12: -0.3217 REMARK 3 L13: -1.2043 L23: -1.3225 REMARK 3 S TENSOR REMARK 3 S11: -0.1474 S12: 0.5385 S13: -0.5681 REMARK 3 S21: -0.2632 S22: -0.1838 S23: -0.4206 REMARK 3 S31: 0.6691 S32: 0.7664 S33: 0.3264 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 225 THROUGH 315 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.1976 -16.8497 -18.9443 REMARK 3 T TENSOR REMARK 3 T11: 0.3761 T22: 1.0519 REMARK 3 T33: 0.6157 T12: 0.0106 REMARK 3 T13: -0.0499 T23: 0.1042 REMARK 3 L TENSOR REMARK 3 L11: 4.1607 L22: 2.2493 REMARK 3 L33: 2.1447 L12: -0.8915 REMARK 3 L13: -0.5406 L23: 0.3418 REMARK 3 S TENSOR REMARK 3 S11: 0.0069 S12: 0.2518 S13: 0.0066 REMARK 3 S21: 0.1691 S22: -0.0469 S23: -0.7733 REMARK 3 S31: 0.2346 S32: 1.2504 S33: 0.0242 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 147 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.6041 -21.4691 -18.0315 REMARK 3 T TENSOR REMARK 3 T11: 0.3523 T22: 0.5083 REMARK 3 T33: 0.4278 T12: -0.0398 REMARK 3 T13: -0.0449 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 6.7320 L22: 2.4560 REMARK 3 L33: 3.4949 L12: -0.2154 REMARK 3 L13: 0.4642 L23: -0.2420 REMARK 3 S TENSOR REMARK 3 S11: 0.0187 S12: 0.7049 S13: -0.3285 REMARK 3 S21: -0.2555 S22: 0.0369 S23: 0.3874 REMARK 3 S31: 0.2245 S32: -0.4414 S33: -0.0772 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 148 THROUGH 188 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.3670 2.3371 -9.4083 REMARK 3 T TENSOR REMARK 3 T11: 0.6988 T22: 0.6541 REMARK 3 T33: 0.8096 T12: 0.0983 REMARK 3 T13: 0.1120 T23: -0.0552 REMARK 3 L TENSOR REMARK 3 L11: 2.9135 L22: 4.5314 REMARK 3 L33: 4.6811 L12: 2.1373 REMARK 3 L13: 0.1057 L23: -0.1839 REMARK 3 S TENSOR REMARK 3 S11: 0.5625 S12: -0.0148 S13: 0.5955 REMARK 3 S21: -0.1343 S22: 0.1298 S23: -0.5560 REMARK 3 S31: -1.1236 S32: -0.4596 S33: -0.7668 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 189 THROUGH 315 ) REMARK 3 ORIGIN FOR THE GROUP (A): -39.2511 -5.5222 -10.0472 REMARK 3 T TENSOR REMARK 3 T11: 0.3680 T22: 0.6364 REMARK 3 T33: 0.6163 T12: 0.1130 REMARK 3 T13: 0.0388 T23: 0.1047 REMARK 3 L TENSOR REMARK 3 L11: 4.5249 L22: 1.9386 REMARK 3 L33: 3.1981 L12: -0.1594 REMARK 3 L13: -0.5358 L23: 0.0855 REMARK 3 S TENSOR REMARK 3 S11: 0.1311 S12: 0.2378 S13: 0.7159 REMARK 3 S21: 0.0615 S22: 0.1331 S23: 0.6374 REMARK 3 S31: -0.6030 S32: -0.9634 S33: -0.2346 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8RWL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292136373. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-SEP-18 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 : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.966 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35833 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 18.25 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.03200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.670 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM HEPES PH 7.5, 30% PEG 300, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 125.65000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.12500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.12500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 188.47500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.12500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.12500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 62.82500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.12500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.12500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 188.47500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.12500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.12500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 62.82500 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 125.65000 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 LYS A 86 REMARK 465 PRO A 87 REMARK 465 GLU A 316 REMARK 465 ARG A 317 REMARK 465 MET B 1 REMARK 465 GLN B 85 REMARK 465 LYS B 86 REMARK 465 PRO B 87 REMARK 465 GLY B 88 REMARK 465 GLN B 89 REMARK 465 PHE B 163 REMARK 465 ASN B 164 REMARK 465 VAL B 165 REMARK 465 HIS B 166 REMARK 465 MET B 167 REMARK 465 GLY B 192 REMARK 465 GLY B 193 REMARK 465 THR B 197 REMARK 465 ARG B 198 REMARK 465 MET B 199 REMARK 465 PRO B 200 REMARK 465 GLY B 201 REMARK 465 TRP B 202 REMARK 465 GLU B 203 REMARK 465 ASP B 204 REMARK 465 PHE B 205 REMARK 465 GLU B 316 REMARK 465 ARG B 317 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 GLN A 85 CG CD OE1 NE2 REMARK 470 ARG A 91 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 140 CG CD CE NZ REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 GLU A 287 CG CD OE1 OE2 REMARK 470 GLU A 289 CG CD OE1 OE2 REMARK 470 GLU A 290 CG CD OE1 OE2 REMARK 470 LYS B 37 CG CD CE NZ REMARK 470 THR B 90 OG1 CG2 REMARK 470 ARG B 91 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 111 CG CD OE1 OE2 REMARK 470 ILE B 159 CG1 CG2 CD1 REMARK 470 LYS B 161 CG CD CE NZ REMARK 470 SER B 168 OG REMARK 470 GLU B 169 CG CD OE1 OE2 REMARK 470 HIS B 171 CG ND1 CD2 CE1 NE2 REMARK 470 ILE B 194 CG1 CG2 CD1 REMARK 470 VAL B 196 CG1 CG2 REMARK 470 ASP B 206 CG OD1 OD2 REMARK 470 VAL B 207 CG1 CG2 REMARK 470 GLU B 209 CG CD OE1 OE2 REMARK 470 ARG B 212 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 216 CG CD OE1 OE2 REMARK 470 GLU B 290 CG CD OE1 OE2 REMARK 470 ILE B 314 CG1 CG2 CD1 REMARK 470 SER B 315 OG 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 O THR A 172 O2 GOL A 402 2.02 REMARK 500 OE2 GLU B 61 O HOH B 501 2.02 REMARK 500 O HOH A 519 O HOH A 538 2.06 REMARK 500 NH2 ARG B 68 O GLU B 107 2.10 REMARK 500 O HOH A 531 O HOH A 553 2.13 REMARK 500 OD2 ASP A 151 ND1 HIS A 178 2.14 REMARK 500 O HOH B 546 O HOH B 566 2.16 REMARK 500 O HOH B 574 O HOH B 580 2.18 REMARK 500 O HOH B 566 O HOH B 576 2.19 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 ALA A 60 139.85 -172.42 REMARK 500 CYS A 66 18.44 -154.06 REMARK 500 TYR A 71 -10.73 -143.27 REMARK 500 GLN A 229 -70.80 -145.98 REMARK 500 GLU A 287 58.94 -93.22 REMARK 500 ALA B 60 130.03 -173.91 REMARK 500 THR B 224 -72.90 -103.59 REMARK 500 GLN B 229 -72.70 -149.05 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 B 583 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH B 584 DISTANCE = 6.97 ANGSTROMS REMARK 525 HOH B 585 DISTANCE = 6.98 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 NA A 406 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 22 O REMARK 620 2 LEU A 24 O 89.7 REMARK 620 3 VAL A 27 O 116.6 74.2 REMARK 620 4 ASP A 59 O 107.9 148.8 117.0 REMARK 620 5 HOH A 510 O 170.2 82.5 67.0 76.7 REMARK 620 6 HOH A 524 O 80.3 73.8 143.4 83.8 91.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 22 O REMARK 620 2 LEU B 24 O 89.7 REMARK 620 3 VAL B 27 O 108.7 82.5 REMARK 620 4 ASP B 59 O 93.6 161.1 113.9 REMARK 620 5 HOH B 526 O 89.9 79.1 153.7 82.2 REMARK 620 6 HOH B 559 O 170.5 90.6 80.7 83.2 80.8 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8RS5 RELATED DB: PDB REMARK 900 DIFFERENT MUTANT OF THE SAME PROTEIN DBREF 8RWL A 1 317 UNP Q8TWG5 MDH_METKA 1 317 DBREF 8RWL B 1 317 UNP Q8TWG5 MDH_METKA 1 317 SEQADV 8RWL GLN A 85 UNP Q8TWG5 ARG 85 ENGINEERED MUTATION SEQADV 8RWL GLN B 85 UNP Q8TWG5 ARG 85 ENGINEERED MUTATION SEQRES 1 A 317 MET SER LYS VAL ALA VAL ILE GLY ALA THR GLY ARG VAL SEQRES 2 A 317 GLY SER THR ALA ALA ALA ARG LEU ALA LEU LEU ASP CYS SEQRES 3 A 317 VAL ASN GLU VAL THR LEU ILE ALA ARG PRO LYS SER VAL SEQRES 4 A 317 ASP LYS LEU ARG GLY LEU ARG ARG ASP ILE LEU ASP SER SEQRES 5 A 317 LEU ALA ALA ALA GLN LYS ASP ALA GLU ILE THR ILE GLY SEQRES 6 A 317 CYS GLU ARG ASP ASP TYR VAL ASP ALA ASP VAL ILE VAL SEQRES 7 A 317 MET THR ALA GLY ILE PRO GLN LYS PRO GLY GLN THR ARG SEQRES 8 A 317 LEU ASP LEU THR LYS ASP ASN ALA ALA ILE ILE LYS LYS SEQRES 9 A 317 TYR LEU GLU GLY VAL ALA GLU GLU ASN PRO GLU ALA ILE SEQRES 10 A 317 VAL LEU VAL VAL THR ASN PRO VAL ASP VAL LEU THR TYR SEQRES 11 A 317 VAL ALA LEU LYS VAL SER GLY LEU PRO LYS ASN ARG VAL SEQRES 12 A 317 ILE GLY LEU GLY THR HIS LEU ASP SER MET ARG PHE LYS SEQRES 13 A 317 VAL LEU ILE ALA LYS HIS PHE ASN VAL HIS MET SER GLU SEQRES 14 A 317 VAL HIS THR ARG ILE ILE GLY GLU HIS GLY ASP THR MET SEQRES 15 A 317 VAL PRO VAL ILE SER SER THR SER VAL GLY GLY ILE PRO SEQRES 16 A 317 VAL THR ARG MET PRO GLY TRP GLU ASP PHE ASP VAL GLU SEQRES 17 A 317 GLU ALA VAL ARG GLU VAL LYS GLU ALA GLY GLN ARG ILE SEQRES 18 A 317 ILE GLU THR TRP GLY GLY SER GLN PHE GLY PRO ALA GLN SEQRES 19 A 317 ALA ILE THR ASN LEU VAL ARG THR ILE LEU GLN ASP GLU SEQRES 20 A 317 ARG ARG VAL LEU THR VAL SER ALA TYR LEU ASP GLY GLU SEQRES 21 A 317 ILE ASP GLY ILE ARG ASP VAL CYS ILE GLY VAL PRO ALA SEQRES 22 A 317 ARG LEU GLY ARG GLU GLY VAL LEU GLU ILE VAL PRO ILE SEQRES 23 A 317 GLU LEU GLU GLU ASP GLU MET ARG ALA PHE ARG ARG SER SEQRES 24 A 317 VAL LYS VAL VAL LYS GLU ALA THR ARG GLU ALA MET GLU SEQRES 25 A 317 ALA ILE SER GLU ARG SEQRES 1 B 317 MET SER LYS VAL ALA VAL ILE GLY ALA THR GLY ARG VAL SEQRES 2 B 317 GLY SER THR ALA ALA ALA ARG LEU ALA LEU LEU ASP CYS SEQRES 3 B 317 VAL ASN GLU VAL THR LEU ILE ALA ARG PRO LYS SER VAL SEQRES 4 B 317 ASP LYS LEU ARG GLY LEU ARG ARG ASP ILE LEU ASP SER SEQRES 5 B 317 LEU ALA ALA ALA GLN LYS ASP ALA GLU ILE THR ILE GLY SEQRES 6 B 317 CYS GLU ARG ASP ASP TYR VAL ASP ALA ASP VAL ILE VAL SEQRES 7 B 317 MET THR ALA GLY ILE PRO GLN LYS PRO GLY GLN THR ARG SEQRES 8 B 317 LEU ASP LEU THR LYS ASP ASN ALA ALA ILE ILE LYS LYS SEQRES 9 B 317 TYR LEU GLU GLY VAL ALA GLU GLU ASN PRO GLU ALA ILE SEQRES 10 B 317 VAL LEU VAL VAL THR ASN PRO VAL ASP VAL LEU THR TYR SEQRES 11 B 317 VAL ALA LEU LYS VAL SER GLY LEU PRO LYS ASN ARG VAL SEQRES 12 B 317 ILE GLY LEU GLY THR HIS LEU ASP SER MET ARG PHE LYS SEQRES 13 B 317 VAL LEU ILE ALA LYS HIS PHE ASN VAL HIS MET SER GLU SEQRES 14 B 317 VAL HIS THR ARG ILE ILE GLY GLU HIS GLY ASP THR MET SEQRES 15 B 317 VAL PRO VAL ILE SER SER THR SER VAL GLY GLY ILE PRO SEQRES 16 B 317 VAL THR ARG MET PRO GLY TRP GLU ASP PHE ASP VAL GLU SEQRES 17 B 317 GLU ALA VAL ARG GLU VAL LYS GLU ALA GLY GLN ARG ILE SEQRES 18 B 317 ILE GLU THR TRP GLY GLY SER GLN PHE GLY PRO ALA GLN SEQRES 19 B 317 ALA ILE THR ASN LEU VAL ARG THR ILE LEU GLN ASP GLU SEQRES 20 B 317 ARG ARG VAL LEU THR VAL SER ALA TYR LEU ASP GLY GLU SEQRES 21 B 317 ILE ASP GLY ILE ARG ASP VAL CYS ILE GLY VAL PRO ALA SEQRES 22 B 317 ARG LEU GLY ARG GLU GLY VAL LEU GLU ILE VAL PRO ILE SEQRES 23 B 317 GLU LEU GLU GLU ASP GLU MET ARG ALA PHE ARG ARG SER SEQRES 24 B 317 VAL LYS VAL VAL LYS GLU ALA THR ARG GLU ALA MET GLU SEQRES 25 B 317 ALA ILE SER GLU ARG HET NDP A 401 74 HET GOL A 402 14 HET GOL A 403 14 HET CL A 404 1 HET CL A 405 1 HET NA A 406 1 HET NDP B 401 74 HET GOL B 402 14 HET GOL B 403 14 HET CL B 404 1 HET NA B 405 1 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NDP 2(C21 H30 N7 O17 P3) FORMUL 4 GOL 4(C3 H8 O3) FORMUL 6 CL 3(CL 1-) FORMUL 8 NA 2(NA 1+) FORMUL 14 HOH *142(H2 O) HELIX 1 AA1 GLY A 11 ALA A 22 1 12 HELIX 2 AA2 ARG A 35 LYS A 37 5 3 HELIX 3 AA3 SER A 38 GLN A 57 1 20 HELIX 4 AA4 GLU A 67 TYR A 71 5 5 HELIX 5 AA5 THR A 90 GLU A 107 1 18 HELIX 6 AA6 GLY A 108 ASN A 113 1 6 HELIX 7 AA7 PRO A 124 GLY A 137 1 14 HELIX 8 AA8 PRO A 139 ASN A 141 5 3 HELIX 9 AA9 THR A 148 ASN A 164 1 17 HELIX 10 AB1 HIS A 166 SER A 168 5 3 HELIX 11 AB2 ILE A 186 SER A 188 5 3 HELIX 12 AB3 THR A 197 MET A 199 5 3 HELIX 13 AB4 GLY A 201 PHE A 205 5 5 HELIX 14 AB5 ASP A 206 TRP A 225 1 20 HELIX 15 AB6 GLN A 229 GLN A 245 1 17 HELIX 16 AB7 GLU A 289 SER A 315 1 27 HELIX 17 AB8 GLY B 11 LEU B 24 1 14 HELIX 18 AB9 ARG B 35 LYS B 37 5 3 HELIX 19 AC1 SER B 38 GLN B 57 1 20 HELIX 20 AC2 GLU B 67 TYR B 71 5 5 HELIX 21 AC3 ARG B 91 GLU B 107 1 17 HELIX 22 AC4 GLY B 108 ASN B 113 1 6 HELIX 23 AC5 PRO B 124 GLY B 137 1 14 HELIX 24 AC6 PRO B 139 ASN B 141 5 3 HELIX 25 AC7 GLY B 147 HIS B 162 1 16 HELIX 26 AC8 ILE B 186 THR B 189 5 4 HELIX 27 AC9 VAL B 207 GLU B 216 1 10 HELIX 28 AD1 GLU B 216 TRP B 225 1 10 HELIX 29 AD2 GLN B 229 GLN B 245 1 17 HELIX 30 AD3 GLU B 289 SER B 315 1 27 SHEET 1 AA1 6 GLU A 61 GLY A 65 0 SHEET 2 AA1 6 GLU A 29 ILE A 33 1 N LEU A 32 O THR A 63 SHEET 3 AA1 6 LYS A 3 ILE A 7 1 N VAL A 4 O GLU A 29 SHEET 4 AA1 6 VAL A 76 MET A 79 1 O VAL A 78 N ALA A 5 SHEET 5 AA1 6 ILE A 117 VAL A 120 1 O ILE A 117 N ILE A 77 SHEET 6 AA1 6 VAL A 143 GLY A 145 1 O ILE A 144 N VAL A 120 SHEET 1 AA2 3 VAL A 170 HIS A 171 0 SHEET 2 AA2 3 SER A 190 VAL A 191 -1 O SER A 190 N HIS A 171 SHEET 3 AA2 3 ILE A 194 PRO A 195 -1 O ILE A 194 N VAL A 191 SHEET 1 AA3 2 ILE A 174 ILE A 175 0 SHEET 2 AA3 2 VAL A 183 PRO A 184 -1 O VAL A 183 N ILE A 175 SHEET 1 AA4 3 ARG A 249 ASP A 258 0 SHEET 2 AA4 3 ARG A 265 GLY A 276 -1 O VAL A 271 N VAL A 253 SHEET 3 AA4 3 GLY A 279 ILE A 283 -1 O LEU A 281 N ARG A 274 SHEET 1 AA5 6 GLU B 61 GLY B 65 0 SHEET 2 AA5 6 GLU B 29 ILE B 33 1 N LEU B 32 O THR B 63 SHEET 3 AA5 6 LYS B 3 ILE B 7 1 N VAL B 6 O THR B 31 SHEET 4 AA5 6 VAL B 76 MET B 79 1 O VAL B 78 N ALA B 5 SHEET 5 AA5 6 ILE B 117 VAL B 120 1 O LEU B 119 N MET B 79 SHEET 6 AA5 6 VAL B 143 GLY B 145 1 O ILE B 144 N VAL B 120 SHEET 1 AA6 2 ILE B 174 GLY B 176 0 SHEET 2 AA6 2 MET B 182 PRO B 184 -1 O VAL B 183 N ILE B 175 SHEET 1 AA7 3 ARG B 249 ASP B 258 0 SHEET 2 AA7 3 ARG B 265 GLY B 276 -1 O LEU B 275 N ARG B 249 SHEET 3 AA7 3 GLY B 279 ILE B 283 -1 O LEU B 281 N ARG B 274 LINK O ALA A 22 NA NA A 406 1555 1555 2.87 LINK O LEU A 24 NA NA A 406 1555 1555 2.86 LINK O VAL A 27 NA NA A 406 1555 1555 2.46 LINK O ASP A 59 NA NA A 406 1555 1555 2.65 LINK NA NA A 406 O HOH A 510 1555 1555 2.95 LINK NA NA A 406 O HOH A 524 1555 1555 2.08 LINK O ALA B 22 NA NA B 405 1555 1555 2.61 LINK O LEU B 24 NA NA B 405 1555 1555 2.52 LINK O VAL B 27 NA NA B 405 1555 1555 2.46 LINK O ASP B 59 NA NA B 405 1555 1555 2.28 LINK NA NA B 405 O HOH B 526 1555 1555 2.47 LINK NA NA B 405 O HOH B 559 1555 1555 2.76 CISPEP 1 ASN A 123 PRO A 124 0 -3.99 CISPEP 2 ASN B 123 PRO B 124 0 -3.17 CRYST1 78.250 78.250 251.300 90.00 90.00 90.00 P 43 21 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 0.012780 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012780 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003979 0.00000