HEADER TRANSFERASE 07-APR-06 2GMU TITLE CRYSTAL STRUCTURE OF E COLI GDP-4-KETO-6-DEOXY-D-MANNOSE-3-DEHYDRATASE TITLE 2 COMPLEXED WITH PLP-GLUTAMATE KETIMINE INTERMEDIATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE PYRIDOXAMINE 5-PHOSPHATE-DEPENDENT DEHYDRASE, COMPND 3 WBDK; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI O55:H7; SOURCE 3 ORGANISM_TAXID: 244320; SOURCE 4 STRAIN: O55:H7, STRAIN 5A; SOURCE 5 GENE: WBDK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS COLITOSE, DEOXYSUGAR, ASPARTATE AMINOTRANSFERASE, PLP, O-ANTIGEN, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.D.COOK,J.B.THODEN,H.M.HOLDEN REVDAT 5 30-AUG-23 2GMU 1 REMARK SEQADV LINK REVDAT 4 18-OCT-17 2GMU 1 REMARK REVDAT 3 24-FEB-09 2GMU 1 VERSN REVDAT 2 03-OCT-06 2GMU 1 JRNL REVDAT 1 05-SEP-06 2GMU 0 JRNL AUTH P.D.COOK,J.B.THODEN,H.M.HOLDEN JRNL TITL THE STRUCTURE OF GDP-4-KETO-6-DEOXY-D-MANNOSE-3-DEHYDRATASE: JRNL TITL 2 A UNIQUE COENZYME B6-DEPENDENT ENZYME. JRNL REF PROTEIN SCI. V. 15 2093 2006 JRNL REFN ISSN 0961-8368 JRNL PMID 16943443 JRNL DOI 10.1110/PS.062328306 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 3 NUMBER OF REFLECTIONS : 61081 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 6079 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1760 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 61081 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6246 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 295 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.009 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.600 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : ENGH & HUBER REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GMU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037307. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : SUPPER MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS HI-STAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72854 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05460 REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.31000 REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2GMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 3400, 0.05 M MES, 0.2 M MGCL2, REMARK 280 0.1 M NACL, 1 MM PYRIDOXAL-5-PHOSPHATE, 2 MM GLUTAMATE, 2 MM GDP, REMARK 280 PH 6.0, BATCH, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 37.45000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.45000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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 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 32 CD GLU A 32 OE2 0.073 REMARK 500 GLU A 117 CD GLU A 117 OE2 0.070 REMARK 500 GLU A 121 CD GLU A 121 OE2 0.072 REMARK 500 GLU A 278 CD GLU A 278 OE2 0.069 REMARK 500 GLU A 321 CD GLU A 321 OE2 0.076 REMARK 500 GLU A 385 CD GLU A 385 OE2 0.070 REMARK 500 GLU B 32 CD GLU B 32 OE2 0.070 REMARK 500 GLU B 117 CD GLU B 117 OE2 0.071 REMARK 500 GLU B 121 CD GLU B 121 OE2 0.066 REMARK 500 GLU B 203 CD GLU B 203 OE2 0.069 REMARK 500 GLU B 237 CD GLU B 237 OE2 0.066 REMARK 500 GLU B 321 CD GLU B 321 OE2 0.066 REMARK 500 GLU B 385 CD GLU B 385 OE2 0.071 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 12 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 24 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 79 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 115 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 115 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 125 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 153 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 159 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 213 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ASP A 234 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 234 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ASP A 286 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 286 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 291 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 311 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 343 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 349 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 357 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 357 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 378 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP B 12 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 12 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP B 13 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP B 108 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 108 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 115 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP B 125 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP B 125 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP B 143 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP B 153 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 SER B 187 N - CA - CB ANGL. DEV. = 9.6 DEGREES REMARK 500 ASP B 234 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 282 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP B 291 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP B 311 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP B 357 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 357 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 378 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 378 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 0 -106.75 115.42 REMARK 500 MET A 30 122.28 -33.41 REMARK 500 SER A 87 173.76 175.19 REMARK 500 ARG A 152 160.89 -40.43 REMARK 500 HIS A 188 -160.88 -102.41 REMARK 500 MET A 193 -67.10 89.30 REMARK 500 PHE A 236 -5.78 -58.59 REMARK 500 TRP A 301 68.61 36.48 REMARK 500 VAL A 334 -125.03 60.21 REMARK 500 ASN A 354 -94.40 63.43 REMARK 500 LEU A 387 37.57 -89.18 REMARK 500 HIS B 0 -7.73 -145.37 REMARK 500 SER B 87 -177.80 179.48 REMARK 500 LEU B 112 -1.63 77.77 REMARK 500 ASN B 170 -5.59 71.48 REMARK 500 MET B 193 -68.20 88.13 REMARK 500 HIS B 215 -0.80 61.40 REMARK 500 TRP B 301 75.53 27.95 REMARK 500 VAL B 334 -111.63 63.96 REMARK 500 ASN B 354 -103.38 65.38 REMARK 500 LEU B 387 59.87 -93.78 REMARK 500 REMARK 500 REMARK: NULL 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 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 375 OE2 REMARK 620 2 ASP A 378 OD2 147.4 REMARK 620 3 HOH A 684 O 85.2 62.5 REMARK 620 4 HOH A 685 O 77.6 94.9 72.1 REMARK 620 5 HOH A 686 O 146.1 49.1 94.9 70.3 REMARK 620 6 HOH A 687 O 87.4 120.4 142.9 70.8 72.2 REMARK 620 7 HOH B 561 O 96.2 89.0 105.3 173.4 116.2 111.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDG A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDG B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GMS RELATED DB: PDB REMARK 900 THE STRUCTURE OF GDP-4-KETO-6-D-MANNOSE-3-DEHYDRATASE IN COMPLEX REMARK 900 WITH HYDRATED PLP DBREF 2GMU A 1 388 GB 18266409 AAL67563 1 388 DBREF 2GMU B 1 388 GB 18266409 AAL67563 1 388 SEQADV 2GMU GLY A -1 GB 18266409 CLONING ARTIFACT SEQADV 2GMU HIS A 0 GB 18266409 CLONING ARTIFACT SEQADV 2GMU GLY B -1 GB 18266409 CLONING ARTIFACT SEQADV 2GMU HIS B 0 GB 18266409 CLONING ARTIFACT SEQRES 1 A 390 GLY HIS MET ILE ASN TYR PRO LEU ALA SER SER THR TRP SEQRES 2 A 390 ASP ASP LEU GLU TYR LYS ALA ILE GLN SER VAL LEU ASP SEQRES 3 A 390 SER LYS MET PHE THR MET GLY GLU TYR VAL LYS GLN TYR SEQRES 4 A 390 GLU THR GLN PHE ALA LYS THR PHE GLY SER LYS TYR ALA SEQRES 5 A 390 VAL MET VAL SER SER GLY SER THR ALA ASN LEU LEU MET SEQRES 6 A 390 ILE ALA ALA LEU PHE PHE THR LYS LYS PRO ARG LEU LYS SEQRES 7 A 390 LYS GLY ASP GLU ILE ILE VAL PRO ALA VAL SER TRP SER SEQRES 8 A 390 THR THR TYR TYR PRO LEU GLN GLN TYR GLY LEU ARG VAL SEQRES 9 A 390 LYS PHE VAL ASP ILE ASP ILE ASN THR LEU ASN ILE ASP SEQRES 10 A 390 ILE GLU SER LEU LYS GLU ALA VAL THR ASP SER THR LYS SEQRES 11 A 390 ALA ILE LEU THR VAL ASN LEU LEU GLY ASN PRO ASN ASN SEQRES 12 A 390 PHE ASP GLU ILE ASN LYS ILE ILE GLY GLY ARG ASP ILE SEQRES 13 A 390 ILE LEU LEU GLU ASP ASN CYS GLU SER MET GLY ALA THR SEQRES 14 A 390 PHE ASN ASN LYS CYS ALA GLY THR PHE GLY LEU MET GLY SEQRES 15 A 390 THR PHE SER SER PHE TYR SER HIS HIS ILE ALA THR MET SEQRES 16 A 390 GLU GLY GLY CYS ILE VAL THR ASP ASP GLU GLU ILE TYR SEQRES 17 A 390 HIS ILE LEU LEU CYS ILE ARG ALA HIS GLY TRP THR ARG SEQRES 18 A 390 ASN LEU PRO LYS LYS ASN LYS VAL THR GLY VAL LYS SER SEQRES 19 A 390 ASP ASP GLN PHE GLU GLU SER PHE LYS PHE VAL LEU PRO SEQRES 20 A 390 GLY TYR ASN VAL ARG PRO LEU GLU MET SER GLY ALA ILE SEQRES 21 A 390 GLY ILE GLU GLN LEU LYS LYS LEU PRO ARG PHE ILE SER SEQRES 22 A 390 VAL ARG ARG LYS ASN ALA GLU TYR PHE LEU ASP LYS PHE SEQRES 23 A 390 LYS ASP HIS PRO TYR LEU ASP VAL GLN GLN GLU THR GLY SEQRES 24 A 390 GLU SER SER TRP PHE GLY PHE SER PHE ILE ILE LYS LYS SEQRES 25 A 390 ASP SER GLY VAL ILE ARG LYS GLN LEU VAL GLU ASN LEU SEQRES 26 A 390 ASN SER ALA GLY ILE GLU CYS ARG PRO ILE VAL THR GLY SEQRES 27 A 390 ASN PHE LEU LYS ASN THR ASP VAL LEU LYS TYR PHE ASP SEQRES 28 A 390 TYR THR VAL HIS ASN ASN VAL ASP ASN ALA GLU TYR LEU SEQRES 29 A 390 ASP LYS ASN GLY LEU PHE VAL GLY ASN HIS GLN ILE GLU SEQRES 30 A 390 LEU PHE ASP GLU ILE ASP TYR LEU ARG GLU VAL LEU LYS SEQRES 1 B 390 GLY HIS MET ILE ASN TYR PRO LEU ALA SER SER THR TRP SEQRES 2 B 390 ASP ASP LEU GLU TYR LYS ALA ILE GLN SER VAL LEU ASP SEQRES 3 B 390 SER LYS MET PHE THR MET GLY GLU TYR VAL LYS GLN TYR SEQRES 4 B 390 GLU THR GLN PHE ALA LYS THR PHE GLY SER LYS TYR ALA SEQRES 5 B 390 VAL MET VAL SER SER GLY SER THR ALA ASN LEU LEU MET SEQRES 6 B 390 ILE ALA ALA LEU PHE PHE THR LYS LYS PRO ARG LEU LYS SEQRES 7 B 390 LYS GLY ASP GLU ILE ILE VAL PRO ALA VAL SER TRP SER SEQRES 8 B 390 THR THR TYR TYR PRO LEU GLN GLN TYR GLY LEU ARG VAL SEQRES 9 B 390 LYS PHE VAL ASP ILE ASP ILE ASN THR LEU ASN ILE ASP SEQRES 10 B 390 ILE GLU SER LEU LYS GLU ALA VAL THR ASP SER THR LYS SEQRES 11 B 390 ALA ILE LEU THR VAL ASN LEU LEU GLY ASN PRO ASN ASN SEQRES 12 B 390 PHE ASP GLU ILE ASN LYS ILE ILE GLY GLY ARG ASP ILE SEQRES 13 B 390 ILE LEU LEU GLU ASP ASN CYS GLU SER MET GLY ALA THR SEQRES 14 B 390 PHE ASN ASN LYS CYS ALA GLY THR PHE GLY LEU MET GLY SEQRES 15 B 390 THR PHE SER SER PHE TYR SER HIS HIS ILE ALA THR MET SEQRES 16 B 390 GLU GLY GLY CYS ILE VAL THR ASP ASP GLU GLU ILE TYR SEQRES 17 B 390 HIS ILE LEU LEU CYS ILE ARG ALA HIS GLY TRP THR ARG SEQRES 18 B 390 ASN LEU PRO LYS LYS ASN LYS VAL THR GLY VAL LYS SER SEQRES 19 B 390 ASP ASP GLN PHE GLU GLU SER PHE LYS PHE VAL LEU PRO SEQRES 20 B 390 GLY TYR ASN VAL ARG PRO LEU GLU MET SER GLY ALA ILE SEQRES 21 B 390 GLY ILE GLU GLN LEU LYS LYS LEU PRO ARG PHE ILE SER SEQRES 22 B 390 VAL ARG ARG LYS ASN ALA GLU TYR PHE LEU ASP LYS PHE SEQRES 23 B 390 LYS ASP HIS PRO TYR LEU ASP VAL GLN GLN GLU THR GLY SEQRES 24 B 390 GLU SER SER TRP PHE GLY PHE SER PHE ILE ILE LYS LYS SEQRES 25 B 390 ASP SER GLY VAL ILE ARG LYS GLN LEU VAL GLU ASN LEU SEQRES 26 B 390 ASN SER ALA GLY ILE GLU CYS ARG PRO ILE VAL THR GLY SEQRES 27 B 390 ASN PHE LEU LYS ASN THR ASP VAL LEU LYS TYR PHE ASP SEQRES 28 B 390 TYR THR VAL HIS ASN ASN VAL ASP ASN ALA GLU TYR LEU SEQRES 29 B 390 ASP LYS ASN GLY LEU PHE VAL GLY ASN HIS GLN ILE GLU SEQRES 30 B 390 LEU PHE ASP GLU ILE ASP TYR LEU ARG GLU VAL LEU LYS HET MG A 601 1 HET PDG A 500 25 HET PDG B 501 25 HETNAM MG MAGNESIUM ION HETNAM PDG N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN- HETNAM 2 PDG 4-YL}METHYL)-D-GLUTAMIC ACID HETSYN PDG N-PYRIDOXYL-D-GLUTAMIC ACID-5'-MONOPHOSPHATE FORMUL 3 MG MG 2+ FORMUL 4 PDG 2(C13 H19 N2 O9 P) FORMUL 6 HOH *295(H2 O) HELIX 1 1 ASP A 12 LYS A 26 1 15 HELIX 2 2 GLY A 31 GLY A 46 1 16 HELIX 3 3 SER A 55 THR A 70 1 16 HELIX 4 4 TRP A 88 TYR A 98 1 11 HELIX 5 5 ASP A 115 VAL A 123 1 9 HELIX 6 6 LEU A 135 ASN A 138 5 4 HELIX 7 7 ASN A 141 GLY A 150 1 10 HELIX 8 8 ASP A 202 ALA A 214 1 13 HELIX 9 9 ASP A 234 SER A 239 1 6 HELIX 10 10 LEU A 252 LYS A 285 1 34 HELIX 11 11 ILE A 315 ALA A 326 1 12 HELIX 12 12 ASN A 337 LYS A 340 5 4 HELIX 13 13 ASN A 341 LYS A 346 1 6 HELIX 14 14 VAL A 356 ASN A 365 1 10 HELIX 15 15 LEU A 376 LEU A 387 1 12 HELIX 16 16 ASP B 12 LYS B 26 1 15 HELIX 17 17 GLY B 31 GLY B 46 1 16 HELIX 18 18 SER B 55 LEU B 67 1 13 HELIX 19 19 TRP B 88 TYR B 98 1 11 HELIX 20 20 ASP B 115 VAL B 123 1 9 HELIX 21 21 LEU B 135 ASN B 138 5 4 HELIX 22 22 ASN B 141 GLY B 150 1 10 HELIX 23 23 ASP B 202 ALA B 214 1 13 HELIX 24 24 ASP B 234 SER B 239 1 6 HELIX 25 25 LEU B 252 LYS B 285 1 34 HELIX 26 26 ILE B 315 ALA B 326 1 12 HELIX 27 27 ASN B 337 LYS B 340 5 4 HELIX 28 28 ASN B 341 LYS B 346 1 6 HELIX 29 29 VAL B 356 ASN B 365 1 10 HELIX 30 30 LEU B 376 LEU B 387 1 12 SHEET 1 A 8 TYR A 49 VAL A 53 0 SHEET 2 A 8 GLY A 196 THR A 200 -1 O GLY A 196 N VAL A 53 SHEET 3 A 8 MET A 179 SER A 183 -1 N GLY A 180 O VAL A 199 SHEET 4 A 8 ILE A 155 ASP A 159 1 N GLU A 158 O THR A 181 SHEET 5 A 8 THR A 127 VAL A 133 1 N LYS A 128 O ILE A 155 SHEET 6 A 8 GLU A 80 PRO A 84 1 N ILE A 82 O LEU A 131 SHEET 7 A 8 ARG A 101 VAL A 105 1 O ARG A 101 N ILE A 81 SHEET 8 A 8 TYR A 350 VAL A 352 1 O THR A 351 N VAL A 102 SHEET 1 B 2 THR A 167 PHE A 168 0 SHEET 2 B 2 LYS A 171 CYS A 172 -1 O LYS A 171 N PHE A 168 SHEET 1 C 2 LYS A 224 ASN A 225 0 SHEET 2 C 2 GLY A 229 VAL A 230 -1 O GLY A 229 N ASN A 225 SHEET 1 D 3 LEU A 290 ASP A 291 0 SHEET 2 D 3 GLY A 303 ILE A 308 -1 O ILE A 307 N ASP A 291 SHEET 3 D 3 GLY A 366 GLY A 370 -1 O VAL A 369 N PHE A 304 SHEET 1 E 8 TYR B 49 VAL B 53 0 SHEET 2 E 8 GLY B 196 THR B 200 -1 O GLY B 196 N VAL B 53 SHEET 3 E 8 MET B 179 SER B 183 -1 N GLY B 180 O VAL B 199 SHEET 4 E 8 ILE B 155 ASP B 159 1 N GLU B 158 O THR B 181 SHEET 5 E 8 THR B 127 VAL B 133 1 N ILE B 130 O ILE B 155 SHEET 6 E 8 GLU B 80 PRO B 84 1 N ILE B 82 O LEU B 131 SHEET 7 E 8 ARG B 101 VAL B 105 1 O LYS B 103 N ILE B 81 SHEET 8 E 8 TYR B 350 VAL B 352 1 O THR B 351 N PHE B 104 SHEET 1 F 2 THR B 167 PHE B 168 0 SHEET 2 F 2 LYS B 171 CYS B 172 -1 O LYS B 171 N PHE B 168 SHEET 1 G 2 LYS B 224 ASN B 225 0 SHEET 2 G 2 GLY B 229 VAL B 230 -1 O GLY B 229 N ASN B 225 SHEET 1 H 3 LEU B 290 VAL B 292 0 SHEET 2 H 3 GLY B 303 ILE B 308 -1 O ILE B 307 N ASP B 291 SHEET 3 H 3 GLY B 366 GLY B 370 -1 O VAL B 369 N PHE B 304 LINK OE2 GLU A 375 MG MG A 601 1555 1555 2.04 LINK OD2 ASP A 378 MG MG A 601 1555 1555 3.03 LINK MG MG A 601 O HOH A 684 1555 1555 2.41 LINK MG MG A 601 O HOH A 685 1555 1555 2.54 LINK MG MG A 601 O HOH A 686 1555 1555 2.16 LINK MG MG A 601 O HOH A 687 1555 1555 1.95 LINK MG MG A 601 O HOH B 561 1555 1455 1.70 SITE 1 AC1 7 GLU A 375 ASP A 378 HOH A 684 HOH A 685 SITE 2 AC1 7 HOH A 686 HOH A 687 HOH B 561 SITE 1 AC2 18 SER A 55 GLY A 56 SER A 57 SER A 87 SITE 2 AC2 18 TRP A 88 THR A 90 THR A 91 ASP A 159 SITE 3 AC2 18 CYS A 161 GLU A 162 SER A 183 PHE A 185 SITE 4 AC2 18 HIS A 188 HOH A 630 HIS B 215 TRP B 217 SITE 5 AC2 18 ASN B 248 ARG B 250 SITE 1 AC3 16 HIS A 215 TRP A 217 ASN A 248 ARG A 250 SITE 2 AC3 16 SER B 55 GLY B 56 SER B 57 SER B 87 SITE 3 AC3 16 TRP B 88 THR B 91 ASP B 159 GLU B 162 SITE 4 AC3 16 SER B 183 PHE B 185 HIS B 188 HOH B 523 CRYST1 74.900 88.000 126.000 90.00 90.00 90.00 P 21 21 21 8 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 0.013351 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011364 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007937 0.00000