HEADER MEMBRANE PROTEIN 06-JAN-10 3LAE TITLE THE CRYSTAL STRUCTURE OF A FUNCTIONALLY UNKNOWN CONSERVED TITLE 2 PROTEIN FROM HAEMOPHILUS INFLUENZAE RD KW20 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0053 PROTEIN HI0107; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 343-420; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UNKNOWN PEPTIDE FRAGMENT; COMPND 8 CHAIN: X; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 3 ORGANISM_TAXID: 727; SOURCE 4 STRAIN: RD KW20; SOURCE 5 GENE: HI0107; 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: PMCSG7; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: PEPTIDE FRAGMENT OF UNKNOWN SOURCE, ITS SOURCE 14 SEQUENCE HAS BEEN ASSIGNED ACCORDING TO ELECTRON DENSITY KEYWDS APC85784.2, CONSERVED PROTEIN, HAEMOPHILUS INFLUENZAE RD KEYWDS 2 KW20, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, KEYWDS 4 CBS DOMAIN, CELL MEMBRANE, MEMBRANE, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,H.LI,M.BARGASSA,S.CLANCY,A.JOACHIMIAK,MIDWEST CENTER AUTHOR 2 FOR STRUCTURAL GENOMICS (MCSG) REVDAT 1 19-JAN-10 3LAE 0 SPRSDE 19-JAN-10 3LAE 2O1R JRNL AUTH K.TAN,H.LI,M.BARGASSA,S.CLANCY,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF A FUNCTIONALLY UNKNOWN JRNL TITL 2 CONSERVED PROTEIN FROM HAEMOPHILUS INFLUENZAE RD JRNL TITL 3 KW20 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 13739 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 680 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 27.6966 - 2.4841 0.99 2845 137 0.1829 0.2348 REMARK 3 2 2.4841 - 1.9719 0.99 2690 153 0.1318 0.1817 REMARK 3 3 1.9719 - 1.7227 0.98 2651 130 0.1259 0.2107 REMARK 3 4 1.7227 - 1.5652 0.95 2571 129 0.1473 0.2211 REMARK 3 5 1.5652 - 1.4530 0.87 2302 131 0.1626 0.2449 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 : 0.43 REMARK 3 B_SOL : 67.03 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08940 REMARK 3 B22 (A**2) : 1.55950 REMARK 3 B33 (A**2) : -1.64900 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 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 : 0.007 795 REMARK 3 ANGLE : 1.052 1096 REMARK 3 CHIRALITY : 0.070 135 REMARK 3 PLANARITY : 0.003 142 REMARK 3 DIHEDRAL : 16.998 324 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 3LAE COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-10. REMARK 100 THE RCSB ID CODE IS RCSB057033. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 0.97929 REMARK 200 MONOCHROMATOR : SI 111 CRYSTAL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14271 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 28.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.7000 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) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.62200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 40.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4M NAH2PO4, 1.6M K2HPO4, 0.1M REMARK 280 IMIDAZOLE, 0.2M NACL, PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 39.55350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.55350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 12.80200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.78150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 12.80200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.78150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.55350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 12.80200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.78150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.55350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 12.80200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.78150 REMARK 290 SMTRY3 8 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: 950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 143 LIES ON A SPECIAL POSITION. 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 GLU A 44 38.68 -98.70 REMARK 500 GLU A 45 136.30 172.93 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 PO4 A 79 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 80 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 81 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 82 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O1R RELATED DB: PDB REMARK 900 THE NEW DEPOSIT IS TO REPLACE 2O1R REMARK 900 RELATED ID: APC85784.2 RELATED DB: TARGETDB DBREF 3LAE A 1 78 UNP Q57017 Y107_HAEIN 343 420 DBREF 3LAE X 1 3 PDB 3LAE 3LAE 1 3 SEQADV 3LAE SER A -2 UNP Q57017 EXPRESSION TAG SEQADV 3LAE ASN A -1 UNP Q57017 EXPRESSION TAG SEQADV 3LAE ALA A 0 UNP Q57017 EXPRESSION TAG SEQRES 1 A 81 SER ASN ALA ILE GLN GLN SER ASP GLY SER MSE ILE ILE SEQRES 2 A 81 ASP GLY SER ALA ASN LEU ARG ASP LEU ASN LYS MSE PHE SEQRES 3 A 81 ASN TRP GLU LEU ASP THR GLU ASP ALA ARG THR PHE ASN SEQRES 4 A 81 GLY LEU ILE LEU GLU HIS LEU GLU GLU ILE PRO ASP GLU SEQRES 5 A 81 GLY THR ILE CYS GLU ILE ASP GLY LEU LEU ILE THR ILE SEQRES 6 A 81 LEU GLU VAL GLY ASP ASN MSE ILE LYS GLN ALA LYS VAL SEQRES 7 A 81 VAL LYS LEU SEQRES 1 X 3 ILE PHE GLY MODRES 3LAE MSE A 8 MET SELENOMETHIONINE MODRES 3LAE MSE A 22 MET SELENOMETHIONINE MODRES 3LAE MSE A 69 MET SELENOMETHIONINE HET MSE A 8 13 HET MSE A 22 13 HET MSE A 69 16 HET PO4 A 79 5 HET EDO A 80 4 HET EDO A 81 4 HET EDO A 82 4 HETNAM MSE SELENOMETHIONINE HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 3 PO4 O4 P 3- FORMUL 4 EDO 3(C2 H6 O2) FORMUL 7 HOH *71(H2 O) HELIX 1 1 ASN A 15 ASN A 24 1 10 HELIX 2 2 THR A 34 LEU A 43 1 10 SHEET 1 A 5 ALA A 0 GLN A 2 0 SHEET 2 A 5 MSE A 8 ASP A 11 -1 O ILE A 9 N ILE A 1 SHEET 3 A 5 MSE A 69 LYS A 77 -1 O ALA A 73 N ILE A 10 SHEET 4 A 5 LEU A 58 GLY A 66 -1 N LEU A 59 O VAL A 76 SHEET 5 A 5 ILE A 52 ILE A 55 -1 N CYS A 53 O ILE A 60 LINK C SER A 7 N MSE A 8 1555 1555 1.33 LINK C MSE A 8 N ILE A 9 1555 1555 1.32 LINK C LYS A 21 N MSE A 22 1555 1555 1.33 LINK C MSE A 22 N PHE A 23 1555 1555 1.33 LINK C ASN A 68 N AMSE A 69 1555 1555 1.33 LINK C ASN A 68 N BMSE A 69 1555 1555 1.33 LINK C AMSE A 69 N ILE A 70 1555 1555 1.33 LINK C BMSE A 69 N ILE A 70 1555 1555 1.33 SITE 1 AC1 7 ASN A 15 ARG A 17 ARG A 33 HOH A 89 SITE 2 AC1 7 HOH A 142 HOH A 143 HOH A 149 SITE 1 AC2 5 SER A 13 GLU A 30 ASP A 31 MSE A 69 SITE 2 AC2 5 HOH A 151 SITE 1 AC3 3 GLY A 66 ASP A 67 HOH A 109 SITE 1 AC4 5 ILE A 9 GLN A 72 LEU A 78 HOH A 92 SITE 2 AC4 5 HOH A 127 CRYST1 25.604 77.563 79.107 90.00 90.00 90.00 C 2 2 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 0.039056 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012893 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012641 0.00000