HEADER OXIDOREDUCTASE 12-OCT-11 3U62 TITLE CRYSTAL STRUCTURE OF SHIKIMATE DEHYDROGENASE FROM THERMOTOGA MARITIMA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHIKIMATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.25; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: AROE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SHIKIMATE PATHWAY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.H.LEE REVDAT 2 01-NOV-23 3U62 1 REMARK REVDAT 1 16-NOV-11 3U62 0 JRNL AUTH H.H.LEE JRNL TITL CRYSTAL STRUCTURE OF SHIKIMATE DEHYDROGENASE FROM THERMOTOGA JRNL TITL 2 MARITIMA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.45 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 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 38992 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 4131 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2036 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21700 REMARK 3 B22 (A**2) : -1.09700 REMARK 3 B33 (A**2) : 0.88000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.948 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.491 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.134 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.187 ; 2.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3U62 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068351. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 6B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9197 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2030 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41086 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 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: CNS REMARK 200 STARTING MODEL: 1NYT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM HEPES BUFFER, 2.0M REMARK 280 AMMONIUM SULFATE, 2%(W/V) POLYETHYLENE GLYCOL 400, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 296K 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 27.10650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.34050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.22250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.34050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.10650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.22250 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 TYR A 8 98.79 -164.86 REMARK 500 VAL A 10 -6.76 -149.07 REMARK 500 THR A 59 -169.85 -122.04 REMARK 500 PRO A 61 41.71 -104.62 REMARK 500 ALA A 116 21.54 -140.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 503 DBREF 3U62 A 1 253 UNP Q9WYI1 AROE_THEMA 1 253 SEQRES 1 A 253 MET LYS PHE CYS ILE ILE GLY TYR PRO VAL ARG HIS SER SEQRES 2 A 253 ILE SER PRO ARG LEU TYR ASN GLU TYR PHE LYS ARG ALA SEQRES 3 A 253 GLY MET ASN HIS SER TYR GLY MET GLU GLU ILE PRO PRO SEQRES 4 A 253 GLU SER PHE ASP THR GLU ILE ARG ARG ILE LEU GLU GLU SEQRES 5 A 253 TYR ASP GLY PHE ASN ALA THR ILE PRO HIS LYS GLU ARG SEQRES 6 A 253 VAL MET ARG TYR VAL GLU PRO SER GLU ASP ALA GLN ARG SEQRES 7 A 253 ILE LYS ALA VAL ASN CYS VAL PHE ARG GLY LYS GLY TYR SEQRES 8 A 253 ASN THR ASP TRP VAL GLY VAL VAL LYS SER LEU GLU GLY SEQRES 9 A 253 VAL GLU VAL LYS GLU PRO VAL VAL VAL VAL GLY ALA GLY SEQRES 10 A 253 GLY ALA ALA ARG ALA VAL ILE TYR ALA LEU LEU GLN MET SEQRES 11 A 253 GLY VAL LYS ASP ILE TRP VAL VAL ASN ARG THR ILE GLU SEQRES 12 A 253 ARG ALA LYS ALA LEU ASP PHE PRO VAL LYS ILE PHE SER SEQRES 13 A 253 LEU ASP GLN LEU ASP GLU VAL VAL LYS LYS ALA LYS SER SEQRES 14 A 253 LEU PHE ASN THR THR SER VAL GLY MET LYS GLY GLU GLU SEQRES 15 A 253 LEU PRO VAL SER ASP ASP SER LEU LYS ASN LEU SER LEU SEQRES 16 A 253 VAL TYR ASP VAL ILE TYR PHE ASP THR PRO LEU VAL VAL SEQRES 17 A 253 LYS ALA ARG LYS LEU GLY VAL LYS HIS ILE ILE LYS GLY SEQRES 18 A 253 ASN LEU MET PHE TYR TYR GLN ALA MET GLU ASN LEU LYS SEQRES 19 A 253 ILE TRP GLY ILE TYR ASP GLU GLU VAL PHE LYS GLU VAL SEQRES 20 A 253 PHE GLY GLU VAL LEU LYS HET SO4 A 500 5 HET SO4 A 501 5 HET SO4 A 502 5 HET SO4 A 503 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 HOH *122(H2 O) HELIX 1 1 ILE A 14 GLY A 27 1 14 HELIX 2 2 PRO A 38 GLU A 40 5 3 HELIX 3 3 SER A 41 TYR A 53 1 13 HELIX 4 4 GLU A 64 VAL A 70 5 7 HELIX 5 5 SER A 73 LYS A 80 1 8 HELIX 6 6 THR A 93 LEU A 102 1 10 HELIX 7 7 GLY A 117 MET A 130 1 14 HELIX 8 8 THR A 141 ALA A 147 1 7 HELIX 9 9 GLN A 159 LYS A 166 1 8 HELIX 10 10 SER A 186 LYS A 191 1 6 HELIX 11 11 THR A 204 GLY A 214 1 11 HELIX 12 12 GLY A 221 TRP A 236 1 16 HELIX 13 13 ASP A 240 GLY A 249 1 10 HELIX 14 14 GLU A 250 LYS A 253 5 4 SHEET 1 A 6 SER A 31 GLU A 36 0 SHEET 2 A 6 LYS A 2 GLY A 7 1 N ILE A 5 O GLU A 35 SHEET 3 A 6 GLY A 55 ALA A 58 1 O ASN A 57 N CYS A 4 SHEET 4 A 6 CYS A 84 PHE A 86 -1 O VAL A 85 N PHE A 56 SHEET 5 A 6 LYS A 89 TYR A 91 -1 O TYR A 91 N CYS A 84 SHEET 6 A 6 GLU A 71 PRO A 72 1 N GLU A 71 O GLY A 90 SHEET 1 B 6 LYS A 153 SER A 156 0 SHEET 2 B 6 ILE A 135 ASN A 139 1 N VAL A 137 O LYS A 153 SHEET 3 B 6 VAL A 111 VAL A 114 1 N VAL A 111 O TRP A 136 SHEET 4 B 6 SER A 169 ASN A 172 1 O PHE A 171 N VAL A 114 SHEET 5 B 6 LEU A 195 ASP A 198 1 O TYR A 197 N LEU A 170 SHEET 6 B 6 HIS A 217 ILE A 219 1 O ILE A 219 N ASP A 198 CISPEP 1 TYR A 8 PRO A 9 0 2.42 CISPEP 2 ILE A 60 PRO A 61 0 -1.88 CISPEP 3 GLU A 109 PRO A 110 0 0.41 SITE 1 AC1 3 SER A 13 ILE A 14 SER A 15 SITE 1 AC2 10 ILE A 60 PRO A 61 HIS A 62 LYS A 63 SITE 2 AC2 10 GLU A 64 GLY A 118 HOH A 264 HOH A 268 SITE 3 AC2 10 HOH A 290 HOH A 334 SITE 1 AC3 6 ARG A 140 ARG A 144 THR A 174 SER A 175 SITE 2 AC3 6 HOH A 298 HOH A 307 SITE 1 AC4 8 GLY A 115 ALA A 116 GLY A 117 ASN A 139 SITE 2 AC4 8 ARG A 140 THR A 141 ARG A 144 HOH A 307 CRYST1 54.213 62.445 68.681 90.00 90.00 90.00 P 21 21 21 4 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 0.018446 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016014 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014560 0.00000