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 MASTER 288 0 8 6 7 0 4 6 0 0 0 14 END