HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 28-APR-10 3MQZ TITLE CRYSTAL STRUCTURE OF CONSERVED PROTEIN DUF1054 FROM PINK SUBAERIAL TITLE 2 BIOFILM MICROBIAL LEPTOSPIRILLUM SP. GROUP II UBA. COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED CONSERVED PROTEIN DUF1054; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEPTOSPIRILLUM RUBARUM; SOURCE 3 ORGANISM_COMMON: LEPTOSPIRILLUM SP. GROUP II UBA; SOURCE 4 ORGANISM_TAXID: 419542; SOURCE 5 GENE: UBAL2_82410687; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ALPHA-BETA FOLD, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, UNKNOWN KEYWDS 3 FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.KIM,X.XU,H.CUI,S.CHIN,A.SAVCHENKO,A.EDWARDS,A.JOACHIMIAK,MIDWEST AUTHOR 2 CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 1 23-JUN-10 3MQZ 0 JRNL AUTH Y.KIM,X.XU,H.CUI,S.CHIN,A.SAVCHENKO,A.EDWARDS,A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURE OF CONSERVED PROTEIN DUF1054 FROM PINK JRNL TITL 2 SUBAERIAL BIOFILM MICROBIAL LEPTOSPIRILLUM SP. GROUP II JRNL TITL 3 UBA. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6_289) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 44069 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2207 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 27.0205 - 2.7967 1.00 4658 232 0.1557 0.1606 REMARK 3 2 2.7967 - 2.2202 1.00 4524 224 0.1544 0.1793 REMARK 3 3 2.2202 - 1.9396 1.00 4451 222 0.1272 0.1566 REMARK 3 4 1.9396 - 1.7623 1.00 4455 204 0.1289 0.1553 REMARK 3 5 1.7623 - 1.6360 1.00 4347 253 0.1238 0.1763 REMARK 3 6 1.6360 - 1.5396 1.00 4360 242 0.1117 0.1640 REMARK 3 7 1.5396 - 1.4625 1.00 4421 230 0.1135 0.1537 REMARK 3 8 1.4625 - 1.3988 0.97 4228 227 0.1224 0.1789 REMARK 3 9 1.3988 - 1.3450 0.84 3645 213 0.1319 0.2068 REMARK 3 10 1.3450 - 1.2985 0.64 2773 160 0.1395 0.2020 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 : 0.40 REMARK 3 B_SOL : 40.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.720 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) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 : 0.008 1972 REMARK 3 ANGLE : 1.244 2700 REMARK 3 CHIRALITY : 0.079 269 REMARK 3 PLANARITY : 0.007 369 REMARK 3 DIHEDRAL : 14.604 777 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 3MQZ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-10. REMARK 100 THE RCSB ID CODE IS RCSB058890. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44135 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28700 REMARK 200 FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL3000, SHELXS,MLPHARE,RESOLVE,SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM FORMATE, 20%PEG3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 17.98350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.91950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.43100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.91950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.98350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.43100 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MSE A 1 REMARK 465 SER A 2 REMARK 465 VAL A 3 REMARK 465 GLN A 4 REMARK 465 THR A 5 REMARK 465 GLY A 211 REMARK 465 SER A 212 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 ARG A 72 -40.70 -137.25 REMARK 500 TYR A 90 -18.29 -148.43 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 CL A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 218 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC41548.0 RELATED DB: TARGETDB DBREF 3MQZ A 1 212 UNP A3ER16 A3ER16_9BACT 1 212 SEQADV 3MQZ SER A -2 UNP A3ER16 EXPRESSION TAG SEQADV 3MQZ ASN A -1 UNP A3ER16 EXPRESSION TAG SEQADV 3MQZ ALA A 0 UNP A3ER16 EXPRESSION TAG SEQRES 1 A 215 SER ASN ALA MSE SER VAL GLN THR ILE GLU ARG LEU GLN SEQRES 2 A 215 ASP TYR LEU LEU PRO GLU TRP VAL SER ILE PHE ASP ILE SEQRES 3 A 215 ALA ASP PHE SER GLY ARG MSE LEU ARG ILE ARG GLY ASP SEQRES 4 A 215 ILE ARG PRO ALA LEU LEU ARG LEU ALA SER ARG LEU ALA SEQRES 5 A 215 GLU LEU LEU ASN GLU SER PRO GLY PRO ARG PRO TRP TYR SEQRES 6 A 215 PRO HIS VAL ALA SER HIS MSE ARG ARG ARG VAL ASN PRO SEQRES 7 A 215 PRO PRO GLU THR TRP LEU ALA LEU GLY PRO GLU LYS ARG SEQRES 8 A 215 GLY TYR LYS SER TYR ALA HIS SER GLY VAL PHE ILE GLY SEQRES 9 A 215 GLY ARG GLY LEU SER VAL ARG PHE ILE LEU LYS ASP GLU SEQRES 10 A 215 ALA ILE GLU GLU ARG LYS ASN LEU GLY ARG TRP MSE SER SEQRES 11 A 215 ARG SER GLY PRO ALA PHE GLU GLN TRP LYS LYS LYS VAL SEQRES 12 A 215 GLY ASP LEU ARG ASP PHE GLY PRO VAL HIS ASP ASP PRO SEQRES 13 A 215 MSE ALA ASP PRO PRO LYS VAL GLU TRP ASP PRO ARG VAL SEQRES 14 A 215 PHE GLY GLU ARG LEU GLY SER LEU LYS SER ALA SER LEU SEQRES 15 A 215 ASP ILE GLY PHE ARG VAL THR PHE ASP THR SER LEU ALA SEQRES 16 A 215 GLY ILE VAL LYS THR ILE ARG THR PHE ASP LEU LEU TYR SEQRES 17 A 215 ALA GLU ALA GLU LYS GLY SER MODRES 3MQZ MSE A 30 MET SELENOMETHIONINE MODRES 3MQZ MSE A 69 MET SELENOMETHIONINE MODRES 3MQZ MSE A 126 MET SELENOMETHIONINE MODRES 3MQZ MSE A 154 MET SELENOMETHIONINE HET MSE A 30 8 HET MSE A 69 8 HET MSE A 126 16 HET MSE A 154 8 HET CL A 215 1 HET CL A 217 1 HET GOL A 218 6 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 CL 2(CL 1-) FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *309(H2 O) HELIX 1 1 ARG A 8 TYR A 12 5 5 HELIX 2 2 LEU A 14 ILE A 23 5 10 HELIX 3 3 ASP A 25 ASP A 36 1 12 HELIX 4 4 ASP A 36 GLU A 54 1 19 HELIX 5 5 ALA A 115 SER A 129 1 15 HELIX 6 6 SER A 129 GLY A 141 1 13 HELIX 7 7 GLY A 147 HIS A 150 5 4 HELIX 8 8 ASP A 163 LEU A 174 1 12 HELIX 9 9 SER A 190 PHE A 201 1 12 HELIX 10 10 PHE A 201 ALA A 208 1 8 SHEET 1 A 6 TYR A 62 VAL A 65 0 SHEET 2 A 6 GLU A 78 GLY A 84 -1 O ALA A 82 N HIS A 64 SHEET 3 A 6 HIS A 95 GLY A 101 -1 O SER A 96 N LEU A 83 SHEET 4 A 6 GLY A 104 LEU A 111 -1 O ILE A 110 N HIS A 95 SHEET 5 A 6 LEU A 179 VAL A 185 -1 O ILE A 181 N PHE A 109 SHEET 6 A 6 ARG A 144 ASP A 145 -1 N ARG A 144 O GLY A 182 LINK C ARG A 29 N MSE A 30 1555 1555 1.33 LINK C MSE A 30 N LEU A 31 1555 1555 1.33 LINK C AHIS A 68 N MSE A 69 1555 1555 1.32 LINK C BHIS A 68 N MSE A 69 1555 1555 1.33 LINK C MSE A 69 N AARG A 70 1555 1555 1.33 LINK C MSE A 69 N BARG A 70 1555 1555 1.33 LINK C TRP A 125 N AMSE A 126 1555 1555 1.33 LINK C TRP A 125 N BMSE A 126 1555 1555 1.33 LINK C AMSE A 126 N ASER A 127 1555 1555 1.32 LINK C BMSE A 126 N BSER A 127 1555 1555 1.33 LINK C PRO A 153 N MSE A 154 1555 1555 1.33 LINK C MSE A 154 N ALA A 155 1555 1555 1.33 SITE 1 AC1 3 SER A 190 HOH A 376 HOH A 395 SITE 1 AC2 5 TYR A 90 LYS A 91 SER A 92 HOH A 291 SITE 2 AC2 5 HOH A 497 SITE 1 AC3 9 GLU A 54 PRO A 56 VAL A 140 PHE A 183 SITE 2 AC3 9 THR A 197 THR A 200 HOH A 293 HOH A 351 SITE 3 AC3 9 HOH A 401 CRYST1 35.967 62.862 81.839 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 0.027803 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015908 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012219 0.00000