HEADER TRANSFERASE 02-NOV-07 3B8X TITLE CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXYMANNOSE-3-DEHYDRATASE (COLD) TITLE 2 H188N MUTANT WITH BOUND GDP-PEROSAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRIDOXAMINE 5-PHOSPHATE-DEPENDENT DEHYDRASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: WBDK; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 244320; SOURCE 4 STRAIN: O55:H7; 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: PET28JT KEYWDS ASPARTATE AMINOTRANSFERASE, COLITOSE, PEROSAMINE, O-ANTIGEN, PLP, KEYWDS 2 PYRIDOXAL PHOSPHATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.D.COOK,H.M.HOLDEN REVDAT 7 30-AUG-23 3B8X 1 REMARK REVDAT 6 20-OCT-21 3B8X 1 REMARK SEQADV LINK REVDAT 5 13-JUL-11 3B8X 1 VERSN REVDAT 4 24-FEB-09 3B8X 1 VERSN REVDAT 3 19-FEB-08 3B8X 1 JRNL REVDAT 2 29-JAN-08 3B8X 1 REMARK REVDAT 1 27-NOV-07 3B8X 0 JRNL AUTH P.D.COOK,H.M.HOLDEN JRNL TITL GDP-4-KETO-6-DEOXY-D-MANNOSE 3-DEHYDRATASE, ACCOMMODATING A JRNL TITL 2 SUGAR SUBSTRATE IN THE ACTIVE SITE. JRNL REF J.BIOL.CHEM. V. 283 4295 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18045869 JRNL DOI 10.1074/JBC.M708893200 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 75464 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 7680 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1770 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) : 83883 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6198 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 126 REMARK 3 SOLVENT ATOMS : 665 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) : 0.013 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.900 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : 17.500; 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 : ISOTROPIC REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3B8X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045226. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MONTELL OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SAINT, SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75510 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 5.780 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 16.2400 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) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.54 REMARK 200 R MERGE FOR SHELL (I) : 0.40800 REMARK 200 R SYM FOR SHELL (I) : 0.40800 REMARK 200 FOR SHELL : 3.160 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: 2GMU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG 3400, 400 MM MGCL2, 100 MM REMARK 280 MES, 2 MM 2-OXOGLUTARATE, 10 MM GDP-PEROSAMINE, PH 6.0, BATCH, REMARK 280 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 31.20550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.97000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.06150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.97000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.20550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.06150 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: 7390 ANGSTROM**2 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 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 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ILE A 2 REMARK 465 GLY B -1 REMARK 465 HIS B 0 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 LEU B 339 CA - CB - CG ANGL. DEV. = -14.4 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 ASP A 12 -166.04 -126.13 REMARK 500 LYS A 26 15.35 58.06 REMARK 500 MET A 30 122.80 -34.82 REMARK 500 SER A 87 -153.50 -173.66 REMARK 500 SER A 87 -153.78 -173.51 REMARK 500 LEU A 112 -0.73 74.78 REMARK 500 THR A 124 -165.19 -124.74 REMARK 500 MET A 193 -69.73 82.30 REMARK 500 PHE A 240 53.56 -115.17 REMARK 500 TRP A 301 70.99 41.36 REMARK 500 VAL A 334 -120.74 44.55 REMARK 500 ASN A 354 -102.77 59.21 REMARK 500 LEU A 387 30.17 -99.01 REMARK 500 MET B 30 121.18 -32.41 REMARK 500 SER B 87 -138.35 -174.98 REMARK 500 LEU B 112 -1.76 75.40 REMARK 500 MET B 193 -70.01 79.42 REMARK 500 HIS B 215 -1.67 64.70 REMARK 500 TRP B 301 75.12 43.94 REMARK 500 VAL B 334 -125.61 46.54 REMARK 500 ASN B 354 -100.28 59.50 REMARK 500 LEU B 387 54.53 -95.12 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 NA A 671 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 6 O REMARK 620 2 ASN A 371 O 104.2 REMARK 620 3 HOH A 743 O 160.7 95.1 REMARK 620 4 HOH A 744 O 86.2 97.8 90.2 REMARK 620 5 HOH A 872 O 93.8 91.5 86.7 170.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 672 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 80 OE2 REMARK 620 2 LYS A 103 NZ 97.1 REMARK 620 3 ALA A 122 O 107.4 72.7 REMARK 620 4 THR A 124 OG1 127.1 124.6 114.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 669 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 175 O REMARK 620 2 ASP A 201 OD2 164.4 REMARK 620 3 HOH A 688 O 105.9 89.0 REMARK 620 4 HOH A 751 O 98.0 85.2 94.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 668 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 242 O REMARK 620 2 ASN B 341 OD1 83.8 REMARK 620 3 ASP B 343 OD1 99.0 107.3 REMARK 620 4 ASP B 343 OD2 96.2 161.2 54.0 REMARK 620 5 HOH B 895 O 169.8 86.8 80.0 91.4 REMARK 620 6 HOH B 959 O 114.3 90.8 143.7 106.1 69.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 673 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 273 NH2 REMARK 620 2 GLN A 373 OE1 115.3 REMARK 620 3 HOH A 831 O 81.3 103.5 REMARK 620 4 HOH A 853 O 101.1 54.9 157.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 666 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU B 6 O REMARK 620 2 ASN B 371 O 103.4 REMARK 620 3 HOH B 694 O 90.6 91.9 REMARK 620 4 HOH B 722 O 161.0 93.4 79.9 REMARK 620 5 HOH B 745 O 89.0 156.4 67.7 72.2 REMARK 620 6 HOH B 751 O 107.4 89.9 161.0 81.2 105.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 670 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 175 O REMARK 620 2 ASP B 201 OD2 177.5 REMARK 620 3 HOH B 765 O 92.4 85.4 REMARK 620 4 HOH B 798 O 88.8 93.6 165.7 REMARK 620 5 HOH B 859 O 88.4 92.9 90.5 75.3 REMARK 620 6 HOH B 892 O 99.2 79.6 93.1 100.8 171.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 667 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 378 OD2 REMARK 620 2 HOH B 847 O 78.0 REMARK 620 3 HOH B 912 O 168.8 92.7 REMARK 620 4 HOH B 995 O 69.7 87.4 116.5 REMARK 620 5 HOH B 997 O 72.9 150.9 116.2 82.1 REMARK 620 6 HOH B1000 O 85.9 93.3 88.6 154.9 85.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 669 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 671 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 672 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 673 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 666 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 667 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 668 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 670 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE G4M A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 674 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 675 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 676 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE G4M B 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GMU RELATED DB: PDB REMARK 900 STRUCTURE OF UREE REMARK 900 RELATED ID: 2R0T RELATED DB: PDB REMARK 900 STRUCTURE OF GDP-4-KETO-6-DEOXYMANNOSE-3-DEHYDRATASE WITH A TRAPPED REMARK 900 PLP-GLUTAMATE GEMINAL DIAMINE DBREF 3B8X A 1 388 UNP Q9F118 Q9F118_ECOLX 1 388 DBREF 3B8X B 1 388 UNP Q9F118 Q9F118_ECOLX 1 388 SEQADV 3B8X GLY A -1 UNP Q9F118 EXPRESSION TAG SEQADV 3B8X HIS A 0 UNP Q9F118 EXPRESSION TAG SEQADV 3B8X ASN A 188 UNP Q9F118 HIS 188 ENGINEERED MUTATION SEQADV 3B8X GLY B -1 UNP Q9F118 EXPRESSION TAG SEQADV 3B8X HIS B 0 UNP Q9F118 EXPRESSION TAG SEQADV 3B8X ASN B 188 UNP Q9F118 HIS 188 ENGINEERED MUTATION 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 ASN 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 ASN 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 NA A 669 1 HET NA A 671 1 HET NA A 672 1 HET NA A 673 1 HET G4M A 500 53 HET EDO A 674 4 HET EDO A 675 4 HET EDO A 676 4 HET NA B 666 1 HET NA B 667 1 HET NA B 668 1 HET NA B 670 1 HET G4M B 500 53 HETNAM NA SODIUM ION HETNAM G4M [(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9- HETNAM 2 G4M YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S, HETNAM 3 G4M 4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5- HETNAM 4 G4M [(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6- HETNAM 5 G4M METHYLTETRAHYDRO-2H-PYRAN-2-YL DIHYDROGEN DIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NA 8(NA 1+) FORMUL 7 G4M 2(C24 H36 N7 O19 P3) FORMUL 8 EDO 3(C2 H6 O2) FORMUL 16 HOH *665(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 LEU A 67 1 13 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 ARG A 213 1 12 HELIX 9 9 LEU A 252 LYS A 285 1 34 HELIX 10 10 ILE A 315 ALA A 326 1 12 HELIX 11 11 ASN A 337 LYS A 340 5 4 HELIX 12 12 ASN A 341 LYS A 346 1 6 HELIX 13 13 VAL A 356 ASN A 365 1 10 HELIX 14 14 LEU A 376 LEU A 387 1 12 HELIX 15 15 ASP B 12 LYS B 26 1 15 HELIX 16 16 GLY B 31 GLY B 46 1 16 HELIX 17 17 SER B 55 LEU B 67 1 13 HELIX 18 18 TRP B 88 TYR B 98 1 11 HELIX 19 19 ASP B 115 VAL B 123 1 9 HELIX 20 20 LEU B 135 ASN B 138 5 4 HELIX 21 21 ASN B 141 GLY B 150 1 10 HELIX 22 22 ASP B 202 ARG B 213 1 12 HELIX 23 23 ASP B 234 PHE B 240 1 7 HELIX 24 24 LEU B 252 LYS B 285 1 34 HELIX 25 25 ILE B 315 GLY B 327 1 13 HELIX 26 26 ASN B 337 LYS B 340 5 4 HELIX 27 27 ASN B 341 LYS B 346 1 6 HELIX 28 28 VAL B 356 ASN B 365 1 10 HELIX 29 29 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 THR A 200 N TYR A 49 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 ILE A 130 O LEU A 157 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 LYS A 103 N ILE A 81 SHEET 8 A 8 ASP A 349 VAL A 352 1 O THR A 351 N PHE A 104 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 VAL A 292 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 THR B 200 N TYR B 49 SHEET 3 E 8 MET B 179 SER B 183 -1 N PHE B 182 O CYS B 197 SHEET 4 E 8 ILE B 155 ASP B 159 1 N GLU B 158 O MET B 179 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 GLU B 80 O LYS B 128 SHEET 7 E 8 ARG B 101 VAL B 105 1 O LYS B 103 N ILE B 81 SHEET 8 E 8 ASP B 349 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 4 LEU B 290 ASP B 291 0 SHEET 2 H 4 GLY B 303 ILE B 308 -1 O ILE B 307 N ASP B 291 SHEET 3 H 4 GLY B 366 GLY B 370 -1 O VAL B 369 N PHE B 304 SHEET 4 H 4 CYS B 330 ARG B 331 -1 N ARG B 331 O PHE B 368 LINK O LEU A 6 NA NA A 671 1555 1555 2.47 LINK OE2 GLU A 80 NA NA A 672 1555 1555 2.39 LINK NZ LYS A 103 NA NA A 672 1555 1555 2.66 LINK O ALA A 122 NA NA A 672 1555 1555 2.81 LINK OG1 THR A 124 NA NA A 672 1555 1555 2.45 LINK O THR A 175 NA NA A 669 1555 1555 2.43 LINK OD2 ASP A 201 NA NA A 669 1555 1555 2.67 LINK O PHE A 242 NA NA B 668 1555 1555 2.41 LINK NH2 ARG A 273 NA NA A 673 1555 1555 2.88 LINK O ASN A 371 NA NA A 671 1555 1555 2.59 LINK OE1 GLN A 373 NA NA A 673 1555 1555 2.93 LINK NA NA A 669 O HOH A 688 1555 1555 2.41 LINK NA NA A 669 O HOH A 751 1555 1555 2.48 LINK NA NA A 671 O HOH A 743 1555 1555 2.60 LINK NA NA A 671 O HOH A 744 1555 1555 2.45 LINK NA NA A 671 O HOH A 872 1555 1555 2.38 LINK NA NA A 673 O HOH A 831 1555 1555 2.42 LINK NA NA A 673 O HOH A 853 1555 1555 2.99 LINK O LEU B 6 NA NA B 666 1555 1555 2.45 LINK O THR B 175 NA NA B 670 1555 1555 2.49 LINK OD2 ASP B 201 NA NA B 670 1555 1555 2.66 LINK OD1 ASN B 341 NA NA B 668 1555 1555 2.32 LINK OD1 ASP B 343 NA NA B 668 1555 1555 2.50 LINK OD2 ASP B 343 NA NA B 668 1555 1555 2.35 LINK O ASN B 371 NA NA B 666 1555 1555 2.63 LINK OD2 ASP B 378 NA NA B 667 1555 1555 2.90 LINK NA NA B 666 O HOH B 694 1555 1555 2.42 LINK NA NA B 666 O HOH B 722 1555 1555 2.54 LINK NA NA B 666 O HOH B 745 1555 1555 2.87 LINK NA NA B 666 O HOH B 751 1555 1555 2.32 LINK NA NA B 667 O HOH B 847 1555 1555 2.39 LINK NA NA B 667 O HOH B 912 1555 1555 2.59 LINK NA NA B 667 O HOH B 995 1555 1555 2.39 LINK NA NA B 667 O HOH B 997 1555 1555 2.45 LINK NA NA B 667 O HOH B1000 1555 1555 2.84 LINK NA NA B 668 O HOH B 895 1555 1555 2.46 LINK NA NA B 668 O HOH B 959 1555 1555 2.35 LINK NA NA B 670 O HOH B 765 1555 1555 2.72 LINK NA NA B 670 O HOH B 798 1555 1555 2.52 LINK NA NA B 670 O HOH B 859 1555 1555 2.52 LINK NA NA B 670 O HOH B 892 1555 1555 2.63 SITE 1 AC1 6 THR A 175 ASP A 201 HOH A 688 HOH A 751 SITE 2 AC1 6 HOH B 717 HOH B 747 SITE 1 AC2 5 LEU A 6 ASN A 371 HOH A 743 HOH A 744 SITE 2 AC2 5 HOH A 872 SITE 1 AC3 6 GLU A 80 LYS A 103 ALA A 122 THR A 124 SITE 2 AC3 6 SER A 126 THR A 127 SITE 1 AC4 6 THR A 10 ASN A 188 ARG A 273 GLN A 373 SITE 2 AC4 6 HOH A 831 HOH A 853 SITE 1 AC5 6 LEU B 6 ASN B 371 HOH B 694 HOH B 722 SITE 2 AC5 6 HOH B 745 HOH B 751 SITE 1 AC6 7 GLU B 375 ASP B 378 HOH B 847 HOH B 912 SITE 2 AC6 7 HOH B 995 HOH B 997 HOH B1000 SITE 1 AC7 5 PHE A 242 ASN B 341 ASP B 343 HOH B 895 SITE 2 AC7 5 HOH B 959 SITE 1 AC8 6 THR B 175 ASP B 201 HOH B 765 HOH B 798 SITE 2 AC8 6 HOH B 859 HOH B 892 SITE 1 AC9 30 SER A 55 GLY A 56 SER A 57 ASN A 60 SITE 2 AC9 30 SER A 87 TRP A 88 THR A 91 ASP A 159 SITE 3 AC9 30 CYS A 161 GLU A 162 SER A 183 PHE A 185 SITE 4 AC9 30 TYR A 186 SER A 187 GLU A 329 ARG A 331 SITE 5 AC9 30 HOH A 677 HOH A 756 HOH A 817 HOH A 885 SITE 6 AC9 30 HOH A 914 LYS B 26 MET B 27 PHE B 28 SITE 7 AC9 30 THR B 29 HIS B 215 ARG B 219 PHE B 240 SITE 8 AC9 30 ASN B 248 HOH B 903 SITE 1 BC1 4 GLU A 38 ALA A 50 TYR A 206 HOH A 811 SITE 1 BC2 5 SER A 9 THR A 10 TRP A 11 ARG A 268 SITE 2 BC2 5 GLN A 373 SITE 1 BC3 3 GLY A 78 GLU A 80 ARG A 101 SITE 1 BC4 30 LYS A 26 MET A 27 PHE A 28 THR A 29 SITE 2 BC4 30 HIS A 215 ARG A 219 PHE A 240 ASN A 248 SITE 3 BC4 30 LEU B 6 SER B 55 GLY B 56 SER B 57 SITE 4 BC4 30 TRP B 88 THR B 90 ASP B 159 CYS B 161 SITE 5 BC4 30 GLU B 162 SER B 183 PHE B 185 TYR B 186 SITE 6 BC4 30 SER B 187 GLU B 329 ARG B 331 HOH B 676 SITE 7 BC4 30 HOH B 705 HOH B 742 HOH B 761 HOH B 864 SITE 8 BC4 30 HOH B 866 HOH B 925 CRYST1 62.411 98.123 119.940 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 0.016023 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008338 0.00000