HEADER OXIDOREDUCTASE 19-JUN-07 2QCU TITLE CRYSTAL STRUCTURE OF GLYCEROL-3-PHOSPHATE DEHYDROGENASE FROM TITLE 2 ESCHERICHIA COLI CAVEAT 2QCU BOG B 800 HAS WRONG CHIRALITY AT ATOM C2 BOG B 800 HAS WRONG CAVEAT 2 2QCU CHIRALITY AT ATOM C3 BOG B 800 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 2QCU C4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AEROBIC GLYCEROL-3-PHOSPHATE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.1.99.5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: GLPD, GLYD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCEROL-3-PHOSHATE DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.I.YEH,U.CHINTE,S.DU REVDAT 5 21-FEB-24 2QCU 1 REMARK HETSYN REVDAT 4 29-JUL-20 2QCU 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 SITE REVDAT 3 18-OCT-17 2QCU 1 REMARK REVDAT 2 24-FEB-09 2QCU 1 VERSN REVDAT 1 15-APR-08 2QCU 0 JRNL AUTH J.I.YEH,U.CHINTE,S.DU JRNL TITL STRUCTURE OF GLYCEROL-3-PHOSPHATE DEHYDROGENASE, AN JRNL TITL 2 ESSENTIAL MONOTOPIC MEMBRANE ENZYME INVOLVED IN RESPIRATION JRNL TITL 3 AND METABOLISM. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 3280 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18296637 JRNL DOI 10.1073/PNAS.0712331105 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 118338 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6272 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8482 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 420 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7997 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 419 REMARK 3 SOLVENT ATOMS : 476 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.03000 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): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.320 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8582 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11552 ; 1.740 ; 1.995 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 998 ;14.085 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 393 ;32.356 ;22.774 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1395 ;18.183 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 78 ;17.041 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1233 ; 0.251 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6340 ; 0.019 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 4272 ; 0.253 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 5733 ; 0.326 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 552 ; 0.167 ; 0.200 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): 53 ; 0.288 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.250 ; 0.200 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): 5079 ; 2.108 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7970 ; 3.034 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4042 ; 4.344 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3582 ; 6.223 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 5 A 499 2 REMARK 3 1 B 5 B 499 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1980 ; 0.08 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 1982 ; 0.56 ; 0.50 REMARK 3 TIGHT THERMAL 1 A (A**2): 1980 ; 0.28 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1982 ; 1.19 ; 2.00 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 2QCU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043437. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SLS; APS REMARK 200 BEAMLINE : X10SA; 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9803; 0.97928, 0.97947, REMARK 200 0.97181 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD; MARMOSAIC REMARK 200 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 136571 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.71200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: PHASER, SOLVE 2.08, RESOLVE 2.08 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M DI-AMMONIUM HYDROGEN PHOSPHATE, REMARK 280 0.1 M TRIS-HCL PH 8.5, 12 % W/V PEG MME 550, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 1.000000 0.000000 0.000000 56.89550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.04850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 96.40050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 56.89550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.04850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 96.40050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 56.89550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.04850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 96.40050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 56.89550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.04850 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 96.40050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLU A 2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LEU A 37 C 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 HOH B 1036 O HOH B 1037 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 GLN A 35 -94.41 -125.12 REMARK 500 ALA A 40 -116.15 -117.23 REMARK 500 ALA A 78 58.80 -144.50 REMARK 500 LYS A 113 16.52 99.57 REMARK 500 ARG A 114 141.27 -23.80 REMARK 500 SER A 116 -17.58 -152.97 REMARK 500 SER A 120 131.50 124.70 REMARK 500 ASP A 143 -157.02 -149.76 REMARK 500 ALA A 205 51.91 -110.94 REMARK 500 LYS A 253 -1.83 81.38 REMARK 500 ASP A 263 -14.21 64.60 REMARK 500 LEU A 319 116.81 43.05 REMARK 500 TRP A 380 -22.45 -153.82 REMARK 500 ILE A 391 -140.43 -109.33 REMARK 500 GLU A 392 58.76 -174.17 REMARK 500 ASP A 396 17.43 132.25 REMARK 500 THR A 420 -65.62 -109.60 REMARK 500 TRP A 459 18.09 58.76 REMARK 500 LEU A 497 -47.60 -161.49 REMARK 500 LEU A 499 -83.25 -115.06 REMARK 500 GLU B 2 -0.53 -163.83 REMARK 500 GLN B 35 -94.21 -126.08 REMARK 500 ALA B 40 -121.82 -114.86 REMARK 500 HIS B 50 -61.73 -109.96 REMARK 500 ALA B 78 58.39 -147.71 REMARK 500 LYS B 113 -59.37 128.79 REMARK 500 ARG B 114 124.97 54.03 REMARK 500 SER B 116 -18.91 -149.60 REMARK 500 ASP B 143 -159.89 -151.31 REMARK 500 ALA B 205 51.44 -107.13 REMARK 500 ILE B 226 109.74 55.70 REMARK 500 LYS B 253 -1.46 77.29 REMARK 500 ASP B 263 -12.43 64.07 REMARK 500 THR B 270 -147.05 -126.46 REMARK 500 LEU B 319 119.78 37.56 REMARK 500 ILE B 376 -109.04 -52.26 REMARK 500 ALA B 379 157.55 -34.24 REMARK 500 TRP B 380 -21.13 -158.31 REMARK 500 ILE B 391 -101.12 -122.15 REMARK 500 GLU B 392 86.60 136.12 REMARK 500 ASP B 394 -66.68 114.62 REMARK 500 LEU B 497 -70.35 -161.87 REMARK 500 ALA B 500 161.11 172.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 496 LEU A 497 116.49 REMARK 500 LEU A 497 SER A 498 146.84 REMARK 500 SER A 498 LEU A 499 -124.81 REMARK 500 LEU A 499 ALA A 500 -132.25 REMARK 500 ARG B 496 LEU B 497 133.65 REMARK 500 LEU B 497 SER B 498 146.20 REMARK 500 SER B 498 LEU B 499 -139.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 2QCU A 1 501 UNP P13035 GLPD_ECOLI 1 501 DBREF 2QCU B 1 501 UNP P13035 GLPD_ECOLI 1 501 SEQRES 1 A 501 MET GLU THR LYS ASP LEU ILE VAL ILE GLY GLY GLY ILE SEQRES 2 A 501 ASN GLY ALA GLY ILE ALA ALA ASP ALA ALA GLY ARG GLY SEQRES 3 A 501 LEU SER VAL LEU MET LEU GLU ALA GLN ASP LEU ALA CYS SEQRES 4 A 501 ALA THR SER SER ALA SER SER LYS LEU ILE HIS GLY GLY SEQRES 5 A 501 LEU ARG TYR LEU GLU HIS TYR GLU PHE ARG LEU VAL SER SEQRES 6 A 501 GLU ALA LEU ALA GLU ARG GLU VAL LEU LEU LYS MET ALA SEQRES 7 A 501 PRO HIS ILE ALA PHE PRO MET ARG PHE ARG LEU PRO HIS SEQRES 8 A 501 ARG PRO HIS LEU ARG PRO ALA TRP MET ILE ARG ILE GLY SEQRES 9 A 501 LEU PHE MET TYR ASP HIS LEU GLY LYS ARG THR SER LEU SEQRES 10 A 501 PRO GLY SER THR GLY LEU ARG PHE GLY ALA ASN SER VAL SEQRES 11 A 501 LEU LYS PRO GLU ILE LYS ARG GLY PHE GLU TYR SER ASP SEQRES 12 A 501 CYS TRP VAL ASP ASP ALA ARG LEU VAL LEU ALA ASN ALA SEQRES 13 A 501 GLN MET VAL VAL ARG LYS GLY GLY GLU VAL LEU THR ARG SEQRES 14 A 501 THR ARG ALA THR SER ALA ARG ARG GLU ASN GLY LEU TRP SEQRES 15 A 501 ILE VAL GLU ALA GLU ASP ILE ASP THR GLY LYS LYS TYR SEQRES 16 A 501 SER TRP GLN ALA ARG GLY LEU VAL ASN ALA THR GLY PRO SEQRES 17 A 501 TRP VAL LYS GLN PHE PHE ASP ASP GLY MET HIS LEU PRO SEQRES 18 A 501 SER PRO TYR GLY ILE ARG LEU ILE LYS GLY SER HIS ILE SEQRES 19 A 501 VAL VAL PRO ARG VAL HIS THR GLN LYS GLN ALA TYR ILE SEQRES 20 A 501 LEU GLN ASN GLU ASP LYS ARG ILE VAL PHE VAL ILE PRO SEQRES 21 A 501 TRP MET ASP GLU PHE SER ILE ILE GLY THR THR ASP VAL SEQRES 22 A 501 GLU TYR LYS GLY ASP PRO LYS ALA VAL LYS ILE GLU GLU SEQRES 23 A 501 SER GLU ILE ASN TYR LEU LEU ASN VAL TYR ASN THR HIS SEQRES 24 A 501 PHE LYS LYS GLN LEU SER ARG ASP ASP ILE VAL TRP THR SEQRES 25 A 501 TYR SER GLY VAL ARG PRO LEU CYS ASP ASP GLU SER ASP SEQRES 26 A 501 SER PRO GLN ALA ILE THR ARG ASP TYR THR LEU ASP ILE SEQRES 27 A 501 HIS ASP GLU ASN GLY LYS ALA PRO LEU LEU SER VAL PHE SEQRES 28 A 501 GLY GLY LYS LEU THR THR TYR ARG LYS LEU ALA GLU HIS SEQRES 29 A 501 ALA LEU GLU LYS LEU THR PRO TYR TYR GLN GLY ILE GLY SEQRES 30 A 501 PRO ALA TRP THR LYS GLU SER VAL LEU PRO GLY GLY ALA SEQRES 31 A 501 ILE GLU GLY ASP ARG ASP ASP TYR ALA ALA ARG LEU ARG SEQRES 32 A 501 ARG ARG TYR PRO PHE LEU THR GLU SER LEU ALA ARG HIS SEQRES 33 A 501 TYR ALA ARG THR TYR GLY SER ASN SER GLU LEU LEU LEU SEQRES 34 A 501 GLY ASN ALA GLY THR VAL SER ASP LEU GLY GLU ASP PHE SEQRES 35 A 501 GLY HIS GLU PHE TYR GLU ALA GLU LEU LYS TYR LEU VAL SEQRES 36 A 501 ASP HIS GLU TRP VAL ARG ARG ALA ASP ASP ALA LEU TRP SEQRES 37 A 501 ARG ARG THR LYS GLN GLY MET TRP LEU ASN ALA ASP GLN SEQRES 38 A 501 GLN SER ARG VAL SER GLN TRP LEU VAL GLU TYR THR GLN SEQRES 39 A 501 GLN ARG LEU SER LEU ALA SER SEQRES 1 B 501 MET GLU THR LYS ASP LEU ILE VAL ILE GLY GLY GLY ILE SEQRES 2 B 501 ASN GLY ALA GLY ILE ALA ALA ASP ALA ALA GLY ARG GLY SEQRES 3 B 501 LEU SER VAL LEU MET LEU GLU ALA GLN ASP LEU ALA CYS SEQRES 4 B 501 ALA THR SER SER ALA SER SER LYS LEU ILE HIS GLY GLY SEQRES 5 B 501 LEU ARG TYR LEU GLU HIS TYR GLU PHE ARG LEU VAL SER SEQRES 6 B 501 GLU ALA LEU ALA GLU ARG GLU VAL LEU LEU LYS MET ALA SEQRES 7 B 501 PRO HIS ILE ALA PHE PRO MET ARG PHE ARG LEU PRO HIS SEQRES 8 B 501 ARG PRO HIS LEU ARG PRO ALA TRP MET ILE ARG ILE GLY SEQRES 9 B 501 LEU PHE MET TYR ASP HIS LEU GLY LYS ARG THR SER LEU SEQRES 10 B 501 PRO GLY SER THR GLY LEU ARG PHE GLY ALA ASN SER VAL SEQRES 11 B 501 LEU LYS PRO GLU ILE LYS ARG GLY PHE GLU TYR SER ASP SEQRES 12 B 501 CYS TRP VAL ASP ASP ALA ARG LEU VAL LEU ALA ASN ALA SEQRES 13 B 501 GLN MET VAL VAL ARG LYS GLY GLY GLU VAL LEU THR ARG SEQRES 14 B 501 THR ARG ALA THR SER ALA ARG ARG GLU ASN GLY LEU TRP SEQRES 15 B 501 ILE VAL GLU ALA GLU ASP ILE ASP THR GLY LYS LYS TYR SEQRES 16 B 501 SER TRP GLN ALA ARG GLY LEU VAL ASN ALA THR GLY PRO SEQRES 17 B 501 TRP VAL LYS GLN PHE PHE ASP ASP GLY MET HIS LEU PRO SEQRES 18 B 501 SER PRO TYR GLY ILE ARG LEU ILE LYS GLY SER HIS ILE SEQRES 19 B 501 VAL VAL PRO ARG VAL HIS THR GLN LYS GLN ALA TYR ILE SEQRES 20 B 501 LEU GLN ASN GLU ASP LYS ARG ILE VAL PHE VAL ILE PRO SEQRES 21 B 501 TRP MET ASP GLU PHE SER ILE ILE GLY THR THR ASP VAL SEQRES 22 B 501 GLU TYR LYS GLY ASP PRO LYS ALA VAL LYS ILE GLU GLU SEQRES 23 B 501 SER GLU ILE ASN TYR LEU LEU ASN VAL TYR ASN THR HIS SEQRES 24 B 501 PHE LYS LYS GLN LEU SER ARG ASP ASP ILE VAL TRP THR SEQRES 25 B 501 TYR SER GLY VAL ARG PRO LEU CYS ASP ASP GLU SER ASP SEQRES 26 B 501 SER PRO GLN ALA ILE THR ARG ASP TYR THR LEU ASP ILE SEQRES 27 B 501 HIS ASP GLU ASN GLY LYS ALA PRO LEU LEU SER VAL PHE SEQRES 28 B 501 GLY GLY LYS LEU THR THR TYR ARG LYS LEU ALA GLU HIS SEQRES 29 B 501 ALA LEU GLU LYS LEU THR PRO TYR TYR GLN GLY ILE GLY SEQRES 30 B 501 PRO ALA TRP THR LYS GLU SER VAL LEU PRO GLY GLY ALA SEQRES 31 B 501 ILE GLU GLY ASP ARG ASP ASP TYR ALA ALA ARG LEU ARG SEQRES 32 B 501 ARG ARG TYR PRO PHE LEU THR GLU SER LEU ALA ARG HIS SEQRES 33 B 501 TYR ALA ARG THR TYR GLY SER ASN SER GLU LEU LEU LEU SEQRES 34 B 501 GLY ASN ALA GLY THR VAL SER ASP LEU GLY GLU ASP PHE SEQRES 35 B 501 GLY HIS GLU PHE TYR GLU ALA GLU LEU LYS TYR LEU VAL SEQRES 36 B 501 ASP HIS GLU TRP VAL ARG ARG ALA ASP ASP ALA LEU TRP SEQRES 37 B 501 ARG ARG THR LYS GLN GLY MET TRP LEU ASN ALA ASP GLN SEQRES 38 B 501 GLN SER ARG VAL SER GLN TRP LEU VAL GLU TYR THR GLN SEQRES 39 B 501 GLN ARG LEU SER LEU ALA SER HET BOG A 700 20 HET BOG A 701 20 HET BOG A 800 20 HET BOG A 801 20 HET SO4 A 802 5 HET SO4 A 803 5 HET PO4 A 804 5 HET FAD A 600 53 HET TAM A 805 11 HET EDO A 806 4 HET IMD A 807 5 HET EDO A 808 4 HET EDO A 809 4 HET EDO A 810 4 HET EDO A 811 4 HET EDO A 812 4 HET EDO A 813 4 HET EDO A 814 4 HET EDO A 815 4 HET EDO A 816 4 HET EDO A 817 4 HET EDO A 818 4 HET EDO A 819 4 HET EDO A 820 4 HET IMD A 821 5 HET EDO A 822 4 HET TAM A 823 11 HET BOG B 700 20 HET BOG B 800 20 HET SO4 B 801 5 HET SO4 B 802 5 HET PO4 B 803 5 HET FAD B 600 53 HET EDO B 804 4 HET EDO B 805 4 HET EDO B 806 4 HET EDO B 807 4 HET EDO B 808 4 HET EDO B 809 4 HET TAM B 810 11 HET EDO B 811 4 HET EDO B 812 4 HET EDO B 813 4 HET EDO B 814 4 HET EDO B 815 4 HET EDO B 816 4 HET EDO B 817 4 HET EDO B 819 4 HET EDO B 820 4 HETNAM BOG OCTYL BETA-D-GLUCOPYRANOSIDE HETNAM SO4 SULFATE ION HETNAM PO4 PHOSPHATE ION HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM TAM TRIS(HYDROXYETHYL)AMINOMETHANE HETNAM EDO 1,2-ETHANEDIOL HETNAM IMD IMIDAZOLE HETSYN BOG BETA-OCTYLGLUCOSIDE; OCTYL BETA-D-GLUCOSIDE; OCTYL D- HETSYN 2 BOG GLUCOSIDE; OCTYL GLUCOSIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 BOG 6(C14 H28 O6) FORMUL 7 SO4 4(O4 S 2-) FORMUL 9 PO4 2(O4 P 3-) FORMUL 10 FAD 2(C27 H33 N9 O15 P2) FORMUL 11 TAM 3(C7 H17 N O3) FORMUL 12 EDO 30(C2 H6 O2) FORMUL 13 IMD 2(C3 H5 N2 1+) FORMUL 52 HOH *476(H2 O) HELIX 1 1 GLY A 12 ARG A 25 1 14 HELIX 2 2 ALA A 40 ALA A 44 5 5 HELIX 3 3 GLY A 52 TYR A 59 5 8 HELIX 4 4 GLU A 60 ALA A 78 1 19 HELIX 5 5 PRO A 97 HIS A 110 1 14 HELIX 6 6 ASP A 147 LYS A 162 1 16 HELIX 7 7 THR A 206 PRO A 208 5 3 HELIX 8 8 TRP A 209 GLY A 217 1 9 HELIX 9 9 ASP A 278 VAL A 282 5 5 HELIX 10 10 GLU A 285 PHE A 300 1 16 HELIX 11 11 SER A 305 ILE A 309 5 5 HELIX 12 12 SER A 326 ILE A 330 5 5 HELIX 13 13 LYS A 354 THR A 356 5 3 HELIX 14 14 THR A 357 THR A 370 1 14 HELIX 15 15 PRO A 371 TYR A 373 5 3 HELIX 16 16 TRP A 380 SER A 384 5 5 HELIX 17 17 ASP A 397 TYR A 406 1 10 HELIX 18 18 THR A 410 TYR A 421 1 12 HELIX 19 19 ASN A 424 GLY A 430 1 7 HELIX 20 20 THR A 434 GLY A 439 5 6 HELIX 21 21 TYR A 447 GLU A 458 1 12 HELIX 22 22 ARG A 462 ARG A 469 1 8 HELIX 23 23 LYS A 472 TRP A 476 5 5 HELIX 24 24 ASN A 478 GLN A 495 1 18 HELIX 25 25 GLY B 12 ARG B 25 1 14 HELIX 26 26 ALA B 40 ALA B 44 5 5 HELIX 27 27 GLY B 52 TYR B 59 5 8 HELIX 28 28 GLU B 60 ALA B 78 1 19 HELIX 29 29 PRO B 97 HIS B 110 1 14 HELIX 30 30 ASP B 147 LYS B 162 1 16 HELIX 31 31 THR B 206 PRO B 208 5 3 HELIX 32 32 TRP B 209 GLY B 217 1 9 HELIX 33 33 ASP B 278 VAL B 282 5 5 HELIX 34 34 GLU B 285 PHE B 300 1 16 HELIX 35 35 SER B 305 ILE B 309 5 5 HELIX 36 36 SER B 326 ILE B 330 5 5 HELIX 37 37 THR B 357 THR B 370 1 14 HELIX 38 38 PRO B 371 TYR B 373 5 3 HELIX 39 39 TRP B 380 SER B 384 5 5 HELIX 40 40 ASP B 397 TYR B 406 1 10 HELIX 41 41 THR B 410 TYR B 421 1 12 HELIX 42 42 ASN B 424 GLY B 430 1 7 HELIX 43 43 THR B 434 GLY B 439 5 6 HELIX 44 44 TYR B 447 GLU B 458 1 12 HELIX 45 45 ARG B 462 ARG B 469 1 8 HELIX 46 46 LYS B 472 TRP B 476 5 5 HELIX 47 47 ASN B 478 GLN B 495 1 18 SHEET 1 A 6 GLU A 165 LEU A 167 0 SHEET 2 A 6 VAL A 29 LEU A 32 1 N MET A 31 O GLU A 165 SHEET 3 A 6 LEU A 6 ILE A 9 1 N VAL A 8 O LEU A 30 SHEET 4 A 6 LEU A 202 ASN A 204 1 O VAL A 203 N ILE A 9 SHEET 5 A 6 LYS A 344 PHE A 351 1 O LEU A 348 N ASN A 204 SHEET 6 A 6 THR A 335 GLU A 341 -1 N HIS A 339 O LEU A 347 SHEET 1 B 8 LEU A 48 ILE A 49 0 SHEET 2 B 8 ARG A 137 VAL A 146 -1 O CYS A 144 N ILE A 49 SHEET 3 B 8 ALA A 82 PRO A 90 -1 N PHE A 87 O TYR A 141 SHEET 4 B 8 ALA A 245 GLN A 249 1 O ALA A 245 N ARG A 86 SHEET 5 B 8 ILE A 255 TRP A 261 -1 O VAL A 256 N LEU A 248 SHEET 6 B 8 PHE A 265 GLY A 269 -1 O GLY A 269 N PHE A 257 SHEET 7 B 8 ILE A 229 PRO A 237 -1 N ILE A 234 O ILE A 268 SHEET 8 B 8 VAL A 273 GLU A 274 -1 O VAL A 273 N LYS A 230 SHEET 1 C 8 THR A 121 ARG A 124 0 SHEET 2 C 8 ARG A 137 VAL A 146 -1 O GLU A 140 N THR A 121 SHEET 3 C 8 ALA A 82 PRO A 90 -1 N PHE A 87 O TYR A 141 SHEET 4 C 8 ALA A 245 GLN A 249 1 O ALA A 245 N ARG A 86 SHEET 5 C 8 ILE A 255 TRP A 261 -1 O VAL A 256 N LEU A 248 SHEET 6 C 8 PHE A 265 GLY A 269 -1 O GLY A 269 N PHE A 257 SHEET 7 C 8 ILE A 229 PRO A 237 -1 N ILE A 234 O ILE A 268 SHEET 8 C 8 TRP A 311 ARG A 317 -1 O TRP A 311 N VAL A 235 SHEET 1 D 3 THR A 170 GLU A 178 0 SHEET 2 D 3 LEU A 181 ASP A 188 -1 O LEU A 181 N GLU A 178 SHEET 3 D 3 LYS A 194 ALA A 199 -1 O TRP A 197 N VAL A 184 SHEET 1 E 4 THR B 3 LYS B 4 0 SHEET 2 E 4 LYS B 194 ALA B 199 1 O GLN B 198 N LYS B 4 SHEET 3 E 4 LEU B 181 ASP B 188 -1 N TRP B 182 O ALA B 199 SHEET 4 E 4 THR B 170 GLU B 178 -1 N GLU B 178 O LEU B 181 SHEET 1 F 6 GLU B 165 LEU B 167 0 SHEET 2 F 6 VAL B 29 LEU B 32 1 N MET B 31 O GLU B 165 SHEET 3 F 6 LEU B 6 ILE B 9 1 N VAL B 8 O LEU B 30 SHEET 4 F 6 LEU B 202 ASN B 204 1 O VAL B 203 N ILE B 9 SHEET 5 F 6 LYS B 344 PHE B 351 1 O LEU B 348 N ASN B 204 SHEET 6 F 6 THR B 335 GLU B 341 -1 N THR B 335 O PHE B 351 SHEET 1 G 8 LEU B 48 ILE B 49 0 SHEET 2 G 8 ARG B 137 VAL B 146 -1 O CYS B 144 N ILE B 49 SHEET 3 G 8 ALA B 82 PRO B 90 -1 N LEU B 89 O PHE B 139 SHEET 4 G 8 ALA B 245 GLN B 249 1 O ALA B 245 N ARG B 86 SHEET 5 G 8 ILE B 255 TRP B 261 -1 O VAL B 256 N LEU B 248 SHEET 6 G 8 PHE B 265 GLY B 269 -1 O GLY B 269 N PHE B 257 SHEET 7 G 8 ILE B 229 PRO B 237 -1 N ILE B 234 O ILE B 268 SHEET 8 G 8 VAL B 273 GLU B 274 -1 O VAL B 273 N LYS B 230 SHEET 1 H 8 THR B 121 ARG B 124 0 SHEET 2 H 8 ARG B 137 VAL B 146 -1 O GLU B 140 N THR B 121 SHEET 3 H 8 ALA B 82 PRO B 90 -1 N LEU B 89 O PHE B 139 SHEET 4 H 8 ALA B 245 GLN B 249 1 O ALA B 245 N ARG B 86 SHEET 5 H 8 ILE B 255 TRP B 261 -1 O VAL B 256 N LEU B 248 SHEET 6 H 8 PHE B 265 GLY B 269 -1 O GLY B 269 N PHE B 257 SHEET 7 H 8 ILE B 229 PRO B 237 -1 N ILE B 234 O ILE B 268 SHEET 8 H 8 TRP B 311 ARG B 317 -1 O TRP B 311 N VAL B 235 CISPEP 1 GLY A 269 THR A 270 0 26.14 CISPEP 2 ARG A 395 ASP A 396 0 -1.63 CISPEP 3 ASP A 396 ASP A 397 0 -1.27 CISPEP 4 GLY B 269 THR B 270 0 0.93 CISPEP 5 ASP B 396 ASP B 397 0 1.32 CRYST1 113.791 114.097 192.801 90.00 90.00 90.00 I 2 2 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 0.008788 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008764 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005187 0.00000