HEADER OXIDOREDUCTASE 21-NOV-23 8X6M TITLE CRYSTAL STRUCTURE OF GLYCEROL DEHYDROGENASE IN THE PRESENCE OF NAD+ TITLE 2 AND GLYCEROL COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCEROL DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GDH,GLDH,(R)-AMINOPROPANOL DEHYDROGENASE,1,2-PROPANEDIOL COMPND 5 DEHYDROGENASE,D-1-AMINO-2-PROPANOL OXIDOREDUCTASE; COMPND 6 EC: 1.1.1.6,1.1.1.75; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: GLDA, B3945, JW5556; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GLYCEROL DEHYDROGENASE, COMPLEX, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.PARK,J.Y.KANG,M.JIN,J.YANG,H.KIM,C.NOH,S.H.EOM REVDAT 1 27-MAR-24 8X6M 0 JRNL AUTH T.PARK,J.Y.KANG,M.JIN,J.YANG,H.KIM,C.NOH,C.H.JUNG,S.H.EOM JRNL TITL STRUCTURAL INSIGHTS INTO THE OCTAMERIZATION OF GLYCEROL JRNL TITL 2 DEHYDROGENASE. JRNL REF PLOS ONE V. 19 00541 2024 JRNL REFN ESSN 1932-6203 JRNL PMID 38483875 JRNL DOI 10.1371/JOURNAL.PONE.0300541 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0415 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 74751 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4016 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5409 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 314 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5438 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 429 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.43000 REMARK 3 B22 (A**2) : 1.43000 REMARK 3 B33 (A**2) : -2.86000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.123 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.869 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5651 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 5352 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7705 ; 1.572 ; 1.648 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12325 ; 0.524 ; 1.566 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 734 ; 6.112 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 26 ; 6.428 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 875 ;14.681 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 903 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6624 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1182 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2939 ; 3.220 ; 3.462 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2939 ; 3.219 ; 3.462 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3672 ; 4.309 ; 6.205 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3673 ; 4.309 ; 6.207 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2712 ; 5.320 ; 4.233 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2713 ; 5.322 ; 4.233 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4034 ; 8.172 ; 7.508 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6534 ; 9.032 ;35.420 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6420 ; 9.035 ;34.490 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8X6M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300041730. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 11C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97942 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78784 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 118.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 26.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 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: 8GOB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA2HPO4-CITRATE (PH 4.2), 200 REMARK 280 MM NACL, AND 10% (W/V) PEG 3000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 65.94650 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 65.94650 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 132.62950 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 65.94650 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 65.94650 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 132.62950 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 65.94650 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 65.94650 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 132.62950 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 65.94650 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 65.94650 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 132.62950 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 65.94650 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 65.94650 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 132.62950 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 65.94650 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 65.94650 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 132.62950 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 65.94650 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 65.94650 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 132.62950 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 65.94650 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 65.94650 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 132.62950 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 31140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 97010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -461.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 -131.89300 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -131.89300 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 -131.89300 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 -131.89300 REMARK 350 BIOMT3 4 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 LEU A 368 REMARK 465 GLU A 369 REMARK 465 HIS A 370 REMARK 465 HIS A 371 REMARK 465 HIS A 372 REMARK 465 HIS A 373 REMARK 465 HIS A 374 REMARK 465 HIS A 375 REMARK 465 LEU B 368 REMARK 465 GLU B 369 REMARK 465 HIS B 370 REMARK 465 HIS B 371 REMARK 465 HIS B 372 REMARK 465 HIS B 373 REMARK 465 HIS B 374 REMARK 465 HIS B 375 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 29 159.94 179.95 REMARK 500 ALA A 118 69.31 -111.00 REMARK 500 ALA A 126 45.33 -96.08 REMARK 500 ASP A 138 -74.26 -106.64 REMARK 500 THR A 238 -72.66 -114.63 REMARK 500 ALA A 251 -126.15 -147.67 REMARK 500 ALA B 126 44.37 -92.34 REMARK 500 ASP B 138 -65.40 -103.99 REMARK 500 ALA B 251 -125.89 -147.77 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 712 DISTANCE = 6.10 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 171 OD1 REMARK 620 2 HIS A 254 NE2 116.2 REMARK 620 3 HIS A 271 NE2 80.6 105.9 REMARK 620 4 GOL A 403 O1 162.4 79.2 104.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 171 OD1 REMARK 620 2 HIS B 254 NE2 107.8 REMARK 620 3 HIS B 271 NE2 92.4 111.3 REMARK 620 N 1 2 DBREF 8X6M A 1 367 UNP P0A9S5 GLDA_ECOLI 1 367 DBREF 8X6M B 1 367 UNP P0A9S5 GLDA_ECOLI 1 367 SEQADV 8X6M LEU A 368 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M GLU A 369 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M HIS A 370 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M HIS A 371 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M HIS A 372 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M HIS A 373 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M HIS A 374 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M HIS A 375 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M LEU B 368 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M GLU B 369 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M HIS B 370 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M HIS B 371 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M HIS B 372 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M HIS B 373 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M HIS B 374 UNP P0A9S5 EXPRESSION TAG SEQADV 8X6M HIS B 375 UNP P0A9S5 EXPRESSION TAG SEQRES 1 A 375 MET ASP ARG ILE ILE GLN SER PRO GLY LYS TYR ILE GLN SEQRES 2 A 375 GLY ALA ASP VAL ILE ASN ARG LEU GLY GLU TYR LEU LYS SEQRES 3 A 375 PRO LEU ALA GLU ARG TRP LEU VAL VAL GLY ASP LYS PHE SEQRES 4 A 375 VAL LEU GLY PHE ALA GLN SER THR VAL GLU LYS SER PHE SEQRES 5 A 375 LYS ASP ALA GLY LEU VAL VAL GLU ILE ALA PRO PHE GLY SEQRES 6 A 375 GLY GLU CYS SER GLN ASN GLU ILE ASP ARG LEU ARG GLY SEQRES 7 A 375 ILE ALA GLU THR ALA GLN CYS GLY ALA ILE LEU GLY ILE SEQRES 8 A 375 GLY GLY GLY LYS THR LEU ASP THR ALA LYS ALA LEU ALA SEQRES 9 A 375 HIS PHE MET GLY VAL PRO VAL ALA ILE ALA PRO THR ILE SEQRES 10 A 375 ALA SER THR ASP ALA PRO CYS SER ALA LEU SER VAL ILE SEQRES 11 A 375 TYR THR ASP GLU GLY GLU PHE ASP ARG TYR LEU LEU LEU SEQRES 12 A 375 PRO ASN ASN PRO ASN MET VAL ILE VAL ASP THR LYS ILE SEQRES 13 A 375 VAL ALA GLY ALA PRO ALA ARG LEU LEU ALA ALA GLY ILE SEQRES 14 A 375 GLY ASP ALA LEU ALA THR TRP PHE GLU ALA ARG ALA CYS SEQRES 15 A 375 SER ARG SER GLY ALA THR THR MET ALA GLY GLY LYS CYS SEQRES 16 A 375 THR GLN ALA ALA LEU ALA LEU ALA GLU LEU CYS TYR ASN SEQRES 17 A 375 THR LEU LEU GLU GLU GLY GLU LYS ALA MET LEU ALA ALA SEQRES 18 A 375 GLU GLN HIS VAL VAL THR PRO ALA LEU GLU ARG VAL ILE SEQRES 19 A 375 GLU ALA ASN THR TYR LEU SER GLY VAL GLY PHE GLU SER SEQRES 20 A 375 GLY GLY LEU ALA ALA ALA HIS ALA VAL HIS ASN GLY LEU SEQRES 21 A 375 THR ALA ILE PRO ASP ALA HIS HIS TYR TYR HIS GLY GLU SEQRES 22 A 375 LYS VAL ALA PHE GLY THR LEU THR GLN LEU VAL LEU GLU SEQRES 23 A 375 ASN ALA PRO VAL GLU GLU ILE GLU THR VAL ALA ALA LEU SEQRES 24 A 375 SER HIS ALA VAL GLY LEU PRO ILE THR LEU ALA GLN LEU SEQRES 25 A 375 ASP ILE LYS GLU ASP VAL PRO ALA LYS MET ARG ILE VAL SEQRES 26 A 375 ALA GLU ALA ALA CYS ALA GLU GLY GLU THR ILE HIS ASN SEQRES 27 A 375 MET PRO GLY GLY ALA THR PRO ASP GLN VAL TYR ALA ALA SEQRES 28 A 375 LEU LEU VAL ALA ASP GLN TYR GLY GLN ARG PHE LEU GLN SEQRES 29 A 375 GLU TRP GLU LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 375 MET ASP ARG ILE ILE GLN SER PRO GLY LYS TYR ILE GLN SEQRES 2 B 375 GLY ALA ASP VAL ILE ASN ARG LEU GLY GLU TYR LEU LYS SEQRES 3 B 375 PRO LEU ALA GLU ARG TRP LEU VAL VAL GLY ASP LYS PHE SEQRES 4 B 375 VAL LEU GLY PHE ALA GLN SER THR VAL GLU LYS SER PHE SEQRES 5 B 375 LYS ASP ALA GLY LEU VAL VAL GLU ILE ALA PRO PHE GLY SEQRES 6 B 375 GLY GLU CYS SER GLN ASN GLU ILE ASP ARG LEU ARG GLY SEQRES 7 B 375 ILE ALA GLU THR ALA GLN CYS GLY ALA ILE LEU GLY ILE SEQRES 8 B 375 GLY GLY GLY LYS THR LEU ASP THR ALA LYS ALA LEU ALA SEQRES 9 B 375 HIS PHE MET GLY VAL PRO VAL ALA ILE ALA PRO THR ILE SEQRES 10 B 375 ALA SER THR ASP ALA PRO CYS SER ALA LEU SER VAL ILE SEQRES 11 B 375 TYR THR ASP GLU GLY GLU PHE ASP ARG TYR LEU LEU LEU SEQRES 12 B 375 PRO ASN ASN PRO ASN MET VAL ILE VAL ASP THR LYS ILE SEQRES 13 B 375 VAL ALA GLY ALA PRO ALA ARG LEU LEU ALA ALA GLY ILE SEQRES 14 B 375 GLY ASP ALA LEU ALA THR TRP PHE GLU ALA ARG ALA CYS SEQRES 15 B 375 SER ARG SER GLY ALA THR THR MET ALA GLY GLY LYS CYS SEQRES 16 B 375 THR GLN ALA ALA LEU ALA LEU ALA GLU LEU CYS TYR ASN SEQRES 17 B 375 THR LEU LEU GLU GLU GLY GLU LYS ALA MET LEU ALA ALA SEQRES 18 B 375 GLU GLN HIS VAL VAL THR PRO ALA LEU GLU ARG VAL ILE SEQRES 19 B 375 GLU ALA ASN THR TYR LEU SER GLY VAL GLY PHE GLU SER SEQRES 20 B 375 GLY GLY LEU ALA ALA ALA HIS ALA VAL HIS ASN GLY LEU SEQRES 21 B 375 THR ALA ILE PRO ASP ALA HIS HIS TYR TYR HIS GLY GLU SEQRES 22 B 375 LYS VAL ALA PHE GLY THR LEU THR GLN LEU VAL LEU GLU SEQRES 23 B 375 ASN ALA PRO VAL GLU GLU ILE GLU THR VAL ALA ALA LEU SEQRES 24 B 375 SER HIS ALA VAL GLY LEU PRO ILE THR LEU ALA GLN LEU SEQRES 25 B 375 ASP ILE LYS GLU ASP VAL PRO ALA LYS MET ARG ILE VAL SEQRES 26 B 375 ALA GLU ALA ALA CYS ALA GLU GLY GLU THR ILE HIS ASN SEQRES 27 B 375 MET PRO GLY GLY ALA THR PRO ASP GLN VAL TYR ALA ALA SEQRES 28 B 375 LEU LEU VAL ALA ASP GLN TYR GLY GLN ARG PHE LEU GLN SEQRES 29 B 375 GLU TRP GLU LEU GLU HIS HIS HIS HIS HIS HIS HET ZN A 401 1 HET NAD A 402 44 HET GOL A 403 6 HET GOL A 404 6 HET ZN B 401 1 HET NAD B 402 44 HETNAM ZN ZINC ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 NAD 2(C21 H27 N7 O14 P2) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 9 HOH *429(H2 O) HELIX 1 AA1 ASP A 16 ASN A 19 5 4 HELIX 2 AA2 ARG A 20 LYS A 26 1 7 HELIX 3 AA3 PRO A 27 ALA A 29 5 3 HELIX 4 AA4 ASP A 37 ALA A 55 1 19 HELIX 5 AA5 SER A 69 GLN A 84 1 16 HELIX 6 AA6 GLY A 93 GLY A 108 1 16 HELIX 7 AA7 ASP A 121 SER A 125 5 5 HELIX 8 AA8 THR A 154 ALA A 160 1 7 HELIX 9 AA9 PRO A 161 GLY A 186 1 26 HELIX 10 AB1 THR A 196 GLN A 223 1 28 HELIX 11 AB2 THR A 227 GLY A 249 1 23 HELIX 12 AB3 ALA A 251 ALA A 262 1 12 HELIX 13 AB4 ILE A 263 HIS A 267 5 5 HELIX 14 AB5 TYR A 270 GLU A 286 1 17 HELIX 15 AB6 PRO A 289 GLY A 304 1 16 HELIX 16 AB7 LEU A 309 ASP A 313 5 5 HELIX 17 AB8 ASP A 317 CYS A 330 1 14 HELIX 18 AB9 GLU A 334 MET A 339 5 6 HELIX 19 AC1 THR A 344 TRP A 366 1 23 HELIX 20 AC2 ASP B 16 ASN B 19 5 4 HELIX 21 AC3 ARG B 20 LYS B 26 1 7 HELIX 22 AC4 PRO B 27 ALA B 29 5 3 HELIX 23 AC5 ASP B 37 GLY B 56 1 20 HELIX 24 AC6 SER B 69 GLN B 84 1 16 HELIX 25 AC7 GLY B 93 MET B 107 1 15 HELIX 26 AC8 THR B 154 ALA B 160 1 7 HELIX 27 AC9 PRO B 161 GLY B 186 1 26 HELIX 28 AD1 THR B 196 HIS B 224 1 29 HELIX 29 AD2 THR B 227 GLY B 249 1 23 HELIX 30 AD3 ALA B 251 THR B 261 1 11 HELIX 31 AD4 ALA B 262 HIS B 267 5 6 HELIX 32 AD5 TYR B 270 GLU B 286 1 17 HELIX 33 AD6 PRO B 289 GLY B 304 1 16 HELIX 34 AD7 LEU B 309 ASP B 313 5 5 HELIX 35 AD8 ASP B 317 CYS B 330 1 14 HELIX 36 AD9 GLU B 334 MET B 339 5 6 HELIX 37 AE1 THR B 344 GLU B 367 1 24 SHEET 1 AA1 7 ARG A 3 GLN A 6 0 SHEET 2 AA1 7 LYS B 10 GLY B 14 -1 O GLN B 13 N ARG A 3 SHEET 3 AA1 7 MET B 149 ASP B 153 1 O VAL B 152 N ILE B 12 SHEET 4 AA1 7 VAL B 111 PRO B 115 1 N ILE B 113 O ILE B 151 SHEET 5 AA1 7 ALA B 87 GLY B 92 1 N ILE B 88 O ALA B 112 SHEET 6 AA1 7 ARG B 31 GLY B 36 1 N VAL B 35 O LEU B 89 SHEET 7 AA1 7 VAL B 58 PRO B 63 1 O ALA B 62 N VAL B 34 SHEET 1 AA2 7 VAL A 58 PRO A 63 0 SHEET 2 AA2 7 ARG A 31 GLY A 36 1 N VAL A 34 O ALA A 62 SHEET 3 AA2 7 ALA A 87 GLY A 92 1 O LEU A 89 N VAL A 35 SHEET 4 AA2 7 VAL A 111 PRO A 115 1 O ALA A 114 N GLY A 90 SHEET 5 AA2 7 MET A 149 ASP A 153 1 O ILE A 151 N ILE A 113 SHEET 6 AA2 7 LYS A 10 GLY A 14 1 N ILE A 12 O VAL A 152 SHEET 7 AA2 7 ARG B 3 GLN B 6 -1 O ILE B 5 N TYR A 11 SHEET 1 AA3 2 LEU A 127 TYR A 131 0 SHEET 2 AA3 2 PHE A 137 LEU A 142 -1 O ARG A 139 N ILE A 130 SHEET 1 AA4 2 LEU B 127 TYR B 131 0 SHEET 2 AA4 2 PHE B 137 LEU B 142 -1 O LEU B 141 N SER B 128 LINK OD1 ASP A 171 ZN ZN A 401 1555 1555 2.66 LINK NE2 HIS A 254 ZN ZN A 401 1555 1555 2.45 LINK NE2 HIS A 271 ZN ZN A 401 1555 1555 2.63 LINK ZN ZN A 401 O1 GOL A 403 1555 1555 2.08 LINK OD1 ASP B 171 ZN ZN B 401 1555 1555 2.53 LINK NE2 HIS B 254 ZN ZN B 401 1555 1555 2.30 LINK NE2 HIS B 271 ZN ZN B 401 1555 1555 2.42 CRYST1 131.893 131.893 265.259 90.00 90.00 90.00 I 4 2 2 32 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 0.007582 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007582 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003770 0.00000