HEADER CELL ADHESION 28-JAN-14 4ONR TITLE CRYSTAL STRUCTURE OF BORRELIA BURGDORFERI DECORIN-BINDING PROTEIN DBPA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DECORIN-BINDING PROTEIN DBPA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORRELIA BURGDORFERI; SOURCE 3 ORGANISM_COMMON: LYME DISEASE SPIROCHETE; SOURCE 4 ORGANISM_TAXID: 139; SOURCE 5 STRAIN: BB297; SOURCE 6 GENE: DBPA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: XL1-BLUE; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS GAG-BINDING PROTEIN, HELICAL BUNDLE PROTEIN, LYME DISEASE, BACTERIAL KEYWDS 2 ADHESIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR D.R.TOMCHICK,R.K.DEKA,J.S.BLEVINS REVDAT 3 28-FEB-24 4ONR 1 REMARK SEQADV LINK REVDAT 2 23-JUL-14 4ONR 1 JRNL REVDAT 1 09-JUL-14 4ONR 0 JRNL AUTH D.E.FORTUNE,Y.P.LIN,R.K.DEKA,A.M.GROSHONG,B.P.MOORE, JRNL AUTH 2 K.E.HAGMAN,J.M.LEONG,D.R.TOMCHICK,J.S.BLEVINS JRNL TITL IDENTIFICATION OF LYSINE RESIDUES IN THE BORRELIA JRNL TITL 2 BURGDORFERI DBPA ADHESIN REQUIRED FOR MURINE INFECTION. JRNL REF INFECT.IMMUN. V. 82 3186 2014 JRNL REFN ISSN 0019-9567 JRNL PMID 24842928 JRNL DOI 10.1128/IAI.02036-14 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 18318 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 937 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 22.7722 - 3.0589 0.99 2560 117 0.1640 0.1778 REMARK 3 2 3.0589 - 2.4289 1.00 2506 153 0.1713 0.1871 REMARK 3 3 2.4289 - 2.1221 1.00 2502 123 0.1499 0.2271 REMARK 3 4 2.1221 - 1.9282 1.00 2519 134 0.1713 0.2155 REMARK 3 5 1.9282 - 1.7900 1.00 2502 131 0.1850 0.2401 REMARK 3 6 1.7900 - 1.6845 1.00 2473 149 0.1925 0.2507 REMARK 3 7 1.6845 - 1.6002 0.93 2319 130 0.2444 0.2730 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.76 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 : 0.010 1156 REMARK 3 ANGLE : 1.135 1551 REMARK 3 CHIRALITY : 0.046 182 REMARK 3 PLANARITY : 0.007 199 REMARK 3 DIHEDRAL : 14.462 449 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -3 THROUGH 75 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.9263 -3.4388 -2.9115 REMARK 3 T TENSOR REMARK 3 T11: 0.3396 T22: 0.2111 REMARK 3 T33: 0.2332 T12: -0.0203 REMARK 3 T13: -0.0183 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 4.8025 L22: 3.7979 REMARK 3 L33: 2.1854 L12: -3.0475 REMARK 3 L13: -0.2893 L23: 0.7921 REMARK 3 S TENSOR REMARK 3 S11: -0.0725 S12: -0.1085 S13: -0.4905 REMARK 3 S21: 0.1505 S22: -0.0503 S23: 0.2134 REMARK 3 S31: 0.4019 S32: -0.0164 S33: 0.1270 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 76 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.7557 5.8793 -2.0040 REMARK 3 T TENSOR REMARK 3 T11: 0.1935 T22: 0.1451 REMARK 3 T33: 0.1363 T12: 0.0000 REMARK 3 T13: 0.0037 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 2.9503 L22: 2.8947 REMARK 3 L33: 2.1755 L12: -0.3489 REMARK 3 L13: -0.4566 L23: 0.1540 REMARK 3 S TENSOR REMARK 3 S11: -0.0281 S12: 0.1369 S13: -0.0274 REMARK 3 S21: -0.2167 S22: -0.1825 S23: -0.0511 REMARK 3 S31: 0.1580 S32: -0.1039 S33: 0.1824 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 130 THROUGH 175 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.1831 9.2423 4.7633 REMARK 3 T TENSOR REMARK 3 T11: 0.1797 T22: 0.1735 REMARK 3 T33: 0.1595 T12: -0.0045 REMARK 3 T13: -0.0065 T23: -0.0073 REMARK 3 L TENSOR REMARK 3 L11: 3.4570 L22: 3.2085 REMARK 3 L33: 2.4647 L12: -0.8154 REMARK 3 L13: -0.4605 L23: 0.5530 REMARK 3 S TENSOR REMARK 3 S11: -0.0524 S12: -0.3044 S13: 0.2223 REMARK 3 S21: 0.0929 S22: 0.0169 S23: -0.2482 REMARK 3 S31: -0.0115 S32: 0.2178 S33: 0.0312 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 4ONR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084724. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-04; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 19-ID; 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97935; 0.97899, 0.97915 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111); REMARK 200 SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : MONOCHROMATOR; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3; SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18358 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 22.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.63100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CHES, 0.05 M NACL, 30% PEG 3000, REMARK 280 10% (W/V) ETHYLENE GLYCOL, PH 9.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 28.97150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.45725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.48575 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 ASP A 65 REMARK 465 LYS A 66 REMARK 465 LYS A 67 REMARK 465 THR A 68 REMARK 465 GLY A 69 REMARK 465 SER A 70 REMARK 465 GLY A 71 REMARK 465 LYS A 176 REMARK 465 LYS A 177 REMARK 465 LYS A 178 REMARK 465 ASN A 179 REMARK 465 THR A 180 REMARK 465 GLU A 181 REMARK 465 ASP A 182 REMARK 465 SER A 183 REMARK 465 THR A 184 REMARK 465 ALA A 185 REMARK 465 LYS A 186 REMARK 465 SER A 187 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 442 O HOH A 464 2.12 REMARK 500 O HOH A 458 O HOH A 468 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ALA A -2 -1.92 -170.13 REMARK 500 PRO A 147 48.43 -82.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A -3 N REMARK 620 2 ALA A -2 N 78.8 REMARK 620 3 MET A -1 N 162.5 84.7 REMARK 620 4 MET A -1 SD 98.0 176.0 98.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 201 DBREF 4ONR A 26 187 UNP Q1W5I8 Q1W5I8_BORBG 26 187 SEQADV 4ONR GLY A -3 UNP Q1W5I8 EXPRESSION TAG SEQADV 4ONR ALA A -2 UNP Q1W5I8 EXPRESSION TAG SEQADV 4ONR MET A -1 UNP Q1W5I8 EXPRESSION TAG SEQADV 4ONR ASP A 0 UNP Q1W5I8 EXPRESSION TAG SEQRES 1 A 166 GLY ALA MET ASP GLY LEU THR GLY ALA THR LYS ILE LYS SEQRES 2 A 166 LEU GLU SER SER ALA LYS ALA ILE VAL ASP GLU ILE ASP SEQRES 3 A 166 ALA ILE LYS LYS LYS ALA ALA SER MET GLY VAL ASN PHE SEQRES 4 A 166 ASP ALA PHE LYS ASP LYS LYS THR GLY SER GLY VAL SER SEQRES 5 A 166 GLU ASN PRO PHE ILE LEU GLU ALA LYS VAL ARG ALA THR SEQRES 6 A 166 THR VAL ALA GLU LYS PHE VAL ILE ALA ILE GLU GLU GLU SEQRES 7 A 166 ALA THR LYS LEU LYS GLU THR GLY SER SER GLY GLU PHE SEQRES 8 A 166 SER ALA MET TYR ASP LEU MET PHE GLU VAL SER LYS PRO SEQRES 9 A 166 LEU GLN GLU LEU GLY ILE GLN GLU MET THR LYS THR VAL SEQRES 10 A 166 SER MET ALA ALA GLU GLU ASN PRO PRO THR THR ALA GLN SEQRES 11 A 166 GLY VAL LEU GLU ILE ALA LYS LYS MET ARG GLU LYS LEU SEQRES 12 A 166 GLN ARG VAL HIS LYS LYS ASN GLN ASP THR LEU LYS LYS SEQRES 13 A 166 LYS ASN THR GLU ASP SER THR ALA LYS SER HET NI A 201 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ FORMUL 3 HOH *171(H2 O) HELIX 1 1 THR A 28 MET A 56 1 29 HELIX 2 2 ASN A 75 LEU A 103 1 29 HELIX 3 3 SER A 108 LEU A 129 1 22 HELIX 4 4 GLU A 133 ASN A 145 1 13 HELIX 5 5 THR A 149 LEU A 175 1 27 LINK N GLY A -3 NI NI A 201 1555 1555 2.26 LINK N ALA A -2 NI NI A 201 1555 1555 1.91 LINK N MET A -1 NI NI A 201 1555 1555 2.01 LINK SD MET A -1 NI NI A 201 1555 1555 2.27 SITE 1 AC1 4 MET A -1 GLY A -3 ALA A -2 ASP A 0 CRYST1 49.524 49.524 57.943 90.00 90.00 90.00 P 43 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 0.020192 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020192 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017258 0.00000