HEADER OXIDOREDUCTASE 09-DEC-10 3PWZ TITLE CRYSTAL STRUCTURE OF AN AEL1 ENZYME FROM PSEUDOMONAS PUTIDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHIKIMATE DEHYDROGENASE 3; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.25; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 GENE: AEL1, AROE-2, AROE3, PP3002, PP_3002; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28A KEYWDS ALPHA-BETA, SHIKIMATE DEHYDROGENASE, ENZYME, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.CHRISTENDAT,J.PEEK REVDAT 3 08-NOV-17 3PWZ 1 REMARK REVDAT 2 19-OCT-11 3PWZ 1 JRNL REVDAT 1 28-SEP-11 3PWZ 0 JRNL AUTH J.PEEK,J.LEE,S.HU,G.SENISTERRA,D.CHRISTENDAT JRNL TITL STRUCTURAL AND MECHANISTIC ANALYSIS OF A NOVEL CLASS OF JRNL TITL 2 SHIKIMATE DEHYDROGENASES: EVIDENCE FOR A CONSERVED CATALYTIC JRNL TITL 3 MECHANISM IN THE SHIKIMATE DEHYDROGENASE FAMILY. JRNL REF BIOCHEMISTRY V. 50 8616 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21846128 JRNL DOI 10.1021/BI200586Y REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 3 NUMBER OF REFLECTIONS : 26029 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 1262 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.1520 - 3.5457 0.99 3249 177 0.1940 0.2157 REMARK 3 2 3.5457 - 2.8150 0.99 3215 151 0.2079 0.2316 REMARK 3 3 2.8150 - 2.4593 0.98 3121 160 0.2201 0.2554 REMARK 3 4 2.4593 - 2.2346 0.96 3104 149 0.2177 0.2600 REMARK 3 5 2.2346 - 2.0744 0.94 3019 158 0.2205 0.2585 REMARK 3 6 2.0744 - 1.9522 0.90 2845 160 0.2365 0.2892 REMARK 3 7 1.9522 - 1.8544 0.78 2482 122 0.2396 0.2679 REMARK 3 8 1.8544 - 1.7737 0.65 2052 109 0.2580 0.3132 REMARK 3 9 1.7737 - 1.7054 0.52 1680 76 0.2719 0.3808 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 42.86 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.52820 REMARK 3 B22 (A**2) : -4.16720 REMARK 3 B33 (A**2) : -5.36100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -6.49220 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2119 REMARK 3 ANGLE : 1.072 2865 REMARK 3 CHIRALITY : 0.070 317 REMARK 3 PLANARITY : 0.005 386 REMARK 3 DIHEDRAL : 15.226 796 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3PWZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062914. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-08 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9177 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27408 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 256.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : 0.08100 REMARK 200 FOR THE DATA SET : 18.3000 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) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 57.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.10500 REMARK 200 R SYM FOR SHELL (I) : 0.46000 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NAHEPES, 2M (NH4)2SO4, AND 1.5% REMARK 280 PEG400, PH 7.5, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 51.64050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.62300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.64050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.62300 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 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 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 93 94.78 -18.18 REMARK 500 ARG A 95 -163.05 -124.84 REMARK 500 PRO A 199 54.05 -66.61 REMARK 500 LEU A 220 96.29 -61.23 REMARK 500 REMARK 500 REMARK: NULL DBREF 3PWZ A 1 272 UNP Q88IJ7 Q88IJ7_PSEPK 1 272 SEQRES 1 A 272 MET SER ASP ARG TYR ALA VAL ILE GLY ARG PRO ILE ASN SEQRES 2 A 272 HIS THR LYS SER PRO LEU ILE HIS GLY LEU PHE ALA GLN SEQRES 3 A 272 ALA SER ASN GLN GLN LEU GLU TYR GLY ALA ILE GLU GLY SEQRES 4 A 272 SER LEU ASP ASP PHE GLU ALA GLN VAL LEU GLN PHE ARG SEQRES 5 A 272 SER GLU GLY GLY LYS GLY MET ASN ILE THR ALA PRO PHE SEQRES 6 A 272 LYS LEU ARG ALA PHE GLU LEU ALA ASP ARG ARG SER GLU SEQRES 7 A 272 ARG ALA GLN LEU ALA ARG ALA ALA ASN ALA LEU LYS PHE SEQRES 8 A 272 GLU ASP GLY ARG ILE VAL ALA GLU ASN PHE ASP GLY ILE SEQRES 9 A 272 GLY LEU LEU ARG ASP ILE GLU GLU ASN LEU GLY GLU PRO SEQRES 10 A 272 LEU ARG ASN ARG ARG VAL LEU LEU LEU GLY ALA GLY GLY SEQRES 11 A 272 ALA VAL ARG GLY ALA LEU LEU PRO PHE LEU GLN ALA GLY SEQRES 12 A 272 PRO SER GLU LEU VAL ILE ALA ASN ARG ASP MET ALA LYS SEQRES 13 A 272 ALA LEU ALA LEU ARG ASN GLU LEU ASP HIS SER ARG LEU SEQRES 14 A 272 ARG ILE SER ARG TYR GLU ALA LEU GLU GLY GLN SER PHE SEQRES 15 A 272 ASP ILE VAL VAL ASN ALA THR SER ALA SER LEU THR ALA SEQRES 16 A 272 ASP LEU PRO PRO LEU PRO ALA ASP VAL LEU GLY GLU ALA SEQRES 17 A 272 ALA LEU ALA TYR GLU LEU ALA TYR GLY LYS GLY LEU THR SEQRES 18 A 272 PRO PHE LEU ARG LEU ALA ARG GLU GLN GLY GLN ALA ARG SEQRES 19 A 272 LEU ALA ASP GLY VAL GLY MET LEU VAL GLU GLN ALA ALA SEQRES 20 A 272 GLU ALA PHE ALA TRP TRP ARG GLY VAL ARG PRO ASP THR SEQRES 21 A 272 ARG ALA VAL ILE ASN GLN LEU THR ILE PRO LEU GLU FORMUL 2 HOH *146(H2 O) HELIX 1 1 LYS A 16 SER A 28 1 13 HELIX 2 2 ASP A 43 GLU A 54 1 12 HELIX 3 3 PHE A 65 ALA A 73 1 9 HELIX 4 4 SER A 77 ARG A 84 1 8 HELIX 5 5 PHE A 101 GLU A 112 1 12 HELIX 6 6 GLY A 129 ALA A 142 1 14 HELIX 7 7 ASP A 153 ASP A 165 1 13 HELIX 8 8 TYR A 174 GLU A 178 5 5 HELIX 9 9 SER A 190 ALA A 195 5 6 HELIX 10 10 PRO A 201 GLY A 206 5 6 HELIX 11 11 THR A 221 GLY A 231 1 11 HELIX 12 12 GLY A 238 GLY A 255 1 18 HELIX 13 13 THR A 260 THR A 268 1 9 SHEET 1 A 6 LEU A 32 GLU A 38 0 SHEET 2 A 6 ASP A 3 GLY A 9 1 N VAL A 7 O ILE A 37 SHEET 3 A 6 GLY A 58 ILE A 61 1 O ASN A 60 N ALA A 6 SHEET 4 A 6 ALA A 88 GLU A 92 -1 O LEU A 89 N MET A 59 SHEET 5 A 6 ARG A 95 GLU A 99 -1 O VAL A 97 N LYS A 90 SHEET 6 A 6 ARG A 75 ARG A 76 1 N ARG A 75 O ALA A 98 SHEET 1 B 6 LEU A 169 SER A 172 0 SHEET 2 B 6 GLU A 146 ALA A 150 1 N LEU A 147 O ARG A 170 SHEET 3 B 6 ARG A 122 LEU A 126 1 N LEU A 125 O VAL A 148 SHEET 4 B 6 ILE A 184 ASN A 187 1 O VAL A 186 N LEU A 124 SHEET 5 B 6 LEU A 210 GLU A 213 1 O TYR A 212 N ASN A 187 SHEET 6 B 6 ARG A 234 ALA A 236 1 O ALA A 236 N GLU A 213 CISPEP 1 ARG A 10 PRO A 11 0 0.62 CISPEP 2 ALA A 63 PRO A 64 0 5.10 CISPEP 3 ASP A 93 GLY A 94 0 -5.95 CRYST1 103.281 49.246 60.510 90.00 114.40 90.00 C 1 2 1 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 0.009682 0.000000 0.004392 0.00000 SCALE2 0.000000 0.020306 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018147 0.00000 MASTER 226 0 0 13 12 0 0 6 0 0 0 21 END