HEADER MEMBRANE PROTEIN 22-JAN-10 3LHH TITLE THE CRYSTAL STRUCTURE OF CBS DOMAIN PROTEIN FROM SHEWANELLA TITLE 2 ONEIDENSIS MR-1. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CBS DOMAIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA ONEIDENSIS; SOURCE 3 ORGANISM_TAXID: 211586; SOURCE 4 STRAIN: MR-1; SOURCE 5 GENE: SO_2815; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P15TV LIC KEYWDS STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, CELL KEYWDS 3 MEMBRANE, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,O.KAGAN,A.SAVCHENKO,A.EDWARDS,A.JOACHIMIAK,MIDWEST AUTHOR 2 CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 1 02-FEB-10 3LHH 0 JRNL AUTH K.TAN,O.KAGAN,A.SAVCHENKO,A.EDWARDS,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF CBS DOMAIN PROTEIN FROM JRNL TITL 2 SHEWANELLA ONEIDENSIS MR-1. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 9492 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 460 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 27.5808 - 3.0258 0.99 3367 153 0.1862 0.2415 REMARK 3 2 3.0258 - 2.4021 0.93 3013 151 0.2131 0.3002 REMARK 3 3 2.4021 - 2.0986 0.83 2652 156 0.2504 0.3155 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 40.80 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.008 1060 REMARK 3 ANGLE : 1.174 1448 REMARK 3 CHIRALITY : 0.068 172 REMARK 3 PLANARITY : 0.006 186 REMARK 3 DIHEDRAL : 20.420 413 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A RESID 53:113 REMARK 3 ORIGIN FOR THE GROUP (A): 11.3278 16.5155 49.3386 REMARK 3 T TENSOR REMARK 3 T11: 0.5033 T22: 0.2917 REMARK 3 T33: 0.3047 T12: -0.0512 REMARK 3 T13: 0.0221 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 0.1629 L22: 2.3074 REMARK 3 L33: 2.0604 L12: 0.3741 REMARK 3 L13: 0.5776 L23: 1.0298 REMARK 3 S TENSOR REMARK 3 S11: -0.0764 S12: 0.0645 S13: 0.1270 REMARK 3 S21: -0.4374 S22: 0.1172 S23: -0.0815 REMARK 3 S31: -0.4913 S32: 0.2630 S33: -0.0264 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 3LHH COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-10. REMARK 100 THE RCSB ID CODE IS RCSB057283. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 0.97937 REMARK 200 MONOCHROMATOR : SI 111 CRYSTAL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10353 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 27.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.79700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.520 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXD/MLPHARE/DM/ARP/WARP/HKL3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRI-NA-CITRATE, 2% MPD, 25% REMARK 280 PEG3350, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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 19.30250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.41100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.62850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.41100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.30250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.62850 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 300 REMARK: EXPERIMENTALLY UNKNOWN. THE CHAIN A IS LIKELY A MONOMER. 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 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 GLY A -1 REMARK 465 HIS A 0 REMARK 465 LEU A 1 REMARK 465 ASP A 2 REMARK 465 ASP A 3 REMARK 465 ASN A 4 REMARK 465 VAL A 5 REMARK 465 THR A 6 REMARK 465 GLN A 7 REMARK 465 GLU A 8 REMARK 465 ASP A 9 REMARK 465 ILE A 10 REMARK 465 GLN A 11 REMARK 465 ALA A 12 REMARK 465 MSE A 13 REMARK 465 LEU A 14 REMARK 465 GLN A 15 REMARK 465 GLU A 16 REMARK 465 GLY A 17 REMARK 465 SER A 18 REMARK 465 SER A 19 REMARK 465 ALA A 20 REMARK 465 GLY A 21 REMARK 465 VAL A 22 REMARK 465 ILE A 23 REMARK 465 GLU A 24 REMARK 465 HIS A 25 REMARK 465 ASN A 26 REMARK 465 GLU A 27 REMARK 465 HIS A 28 REMARK 465 ALA A 29 REMARK 465 MSE A 30 REMARK 465 VAL A 31 REMARK 465 LYS A 32 REMARK 465 ASN A 33 REMARK 465 VAL A 34 REMARK 465 PHE A 35 REMARK 465 ARG A 36 REMARK 465 LEU A 37 REMARK 465 ASP A 38 REMARK 465 GLU A 39 REMARK 465 ARG A 40 REMARK 465 GLN A 166 REMARK 465 GLU A 167 REMARK 465 ASP A 168 REMARK 465 GLY A 169 REMARK 465 SER A 170 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 ASN A 81 -51.51 68.41 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 AMP A 171 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC65307.2 RELATED DB: TARGETDB DBREF 3LHH A 1 168 UNP Q8EDE1 Q8EDE1_SHEON 170 337 SEQADV 3LHH GLY A -1 UNP Q8EDE1 EXPRESSION TAG SEQADV 3LHH HIS A 0 UNP Q8EDE1 EXPRESSION TAG SEQADV 3LHH GLY A 169 UNP Q8EDE1 EXPRESSION TAG SEQADV 3LHH SER A 170 UNP Q8EDE1 EXPRESSION TAG SEQRES 1 A 172 GLY HIS LEU ASP ASP ASN VAL THR GLN GLU ASP ILE GLN SEQRES 2 A 172 ALA MSE LEU GLN GLU GLY SER SER ALA GLY VAL ILE GLU SEQRES 3 A 172 HIS ASN GLU HIS ALA MSE VAL LYS ASN VAL PHE ARG LEU SEQRES 4 A 172 ASP GLU ARG THR ILE SER SER LEU MSE VAL PRO ARG SER SEQRES 5 A 172 ASP ILE VAL PHE LEU ASP LEU ASN LEU PRO LEU ASP ALA SEQRES 6 A 172 ASN LEU ARG THR VAL MSE GLN SER PRO HIS SER ARG PHE SEQRES 7 A 172 PRO VAL CYS ARG ASN ASN VAL ASP ASP MSE VAL GLY ILE SEQRES 8 A 172 ILE SER ALA LYS GLN LEU LEU SER GLU SER ILE ALA GLY SEQRES 9 A 172 GLU ARG LEU GLU LEU VAL ASP LEU VAL LYS ASN CYS ASN SEQRES 10 A 172 PHE VAL PRO ASN SER LEU SER GLY MSE GLU LEU LEU GLU SEQRES 11 A 172 HIS PHE ARG THR THR GLY SER GLN MSE VAL PHE VAL VAL SEQRES 12 A 172 ASP GLU TYR GLY ASP LEU LYS GLY LEU VAL THR LEU GLN SEQRES 13 A 172 ASP MSE MSE ASP ALA LEU THR GLY GLU PHE PHE GLN GLU SEQRES 14 A 172 ASP GLY SER MODRES 3LHH MSE A 46 MET SELENOMETHIONINE MODRES 3LHH MSE A 69 MET SELENOMETHIONINE MODRES 3LHH MSE A 86 MET SELENOMETHIONINE MODRES 3LHH MSE A 124 MET SELENOMETHIONINE MODRES 3LHH MSE A 137 MET SELENOMETHIONINE MODRES 3LHH MSE A 156 MET SELENOMETHIONINE MODRES 3LHH MSE A 157 MET SELENOMETHIONINE HET MSE A 46 8 HET MSE A 69 13 HET MSE A 86 8 HET MSE A 124 8 HET MSE A 137 8 HET MSE A 156 8 HET MSE A 157 8 HET AMP A 171 23 HETNAM MSE SELENOMETHIONINE HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 1 MSE 7(C5 H11 N O2 SE) FORMUL 2 AMP C10 H14 N5 O7 P FORMUL 3 HOH *39(H2 O) HELIX 1 1 SER A 50 ILE A 52 5 3 HELIX 2 2 PRO A 60 GLN A 70 1 11 HELIX 3 3 ALA A 92 ALA A 101 1 10 HELIX 4 4 GLU A 106 VAL A 111 5 6 HELIX 5 5 SER A 122 GLY A 134 1 13 HELIX 6 6 LEU A 153 GLY A 162 1 10 SHEET 1 A 4 VAL A 47 PRO A 48 0 SHEET 2 A 4 LEU A 147 THR A 152 -1 O LEU A 150 N VAL A 47 SHEET 3 A 4 MSE A 137 VAL A 141 -1 N VAL A 140 O LYS A 148 SHEET 4 A 4 ASN A 115 PRO A 118 1 N ASN A 115 O PHE A 139 SHEET 1 B 3 LEU A 55 ASP A 56 0 SHEET 2 B 3 ARG A 75 CYS A 79 1 O CYS A 79 N LEU A 55 SHEET 3 B 3 MSE A 86 SER A 91 -1 O GLY A 88 N VAL A 78 LINK C LEU A 45 N MSE A 46 1555 1555 1.32 LINK C MSE A 46 N VAL A 47 1555 1555 1.33 LINK C VAL A 68 N MSE A 69 1555 1555 1.32 LINK C MSE A 69 N GLN A 70 1555 1555 1.33 LINK C ASP A 85 N MSE A 86 1555 1555 1.33 LINK C MSE A 86 N VAL A 87 1555 1555 1.32 LINK C GLY A 123 N MSE A 124 1555 1555 1.33 LINK C MSE A 124 N GLU A 125 1555 1555 1.33 LINK C GLN A 136 N MSE A 137 1555 1555 1.33 LINK C MSE A 137 N VAL A 138 1555 1555 1.33 LINK C ASP A 155 N MSE A 156 1555 1555 1.33 LINK C MSE A 156 N MSE A 157 1555 1555 1.33 LINK C MSE A 157 N ASP A 158 1555 1555 1.33 SITE 1 AC1 13 ASP A 51 VAL A 53 HIS A 73 SER A 74 SITE 2 AC1 13 ARG A 75 PRO A 77 MSE A 137 THR A 152 SITE 3 AC1 13 GLN A 154 ASP A 155 HOH A 185 HOH A 192 SITE 4 AC1 13 HOH A 194 CRYST1 38.605 55.257 78.822 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 0.025903 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018097 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012687 0.00000