HEADER MOTOR PROTEIN 14-DEC-18 6NDW TITLE CRYSTAL STRUCTURE OF THE WILD TYPE D2 DOMAIN (A168-T344) OF THE TITLE 2 FLAGELLAR HOOK PROTEIN FLGE FROM TREPONEMA DENTICOLA COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAGELLAR HOOK PROTEIN FLGE; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TREPONEMA DENTICOLA; SOURCE 3 ORGANISM_TAXID: 158; SOURCE 4 GENE: FLGE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HOOK, LYSINOALANINE, CROSSLINKING, SPIROCHETES, PERIODONTAL DISEASE, KEYWDS 2 FLGE, MOTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.J.LYNCH,B.R.CRANE REVDAT 5 11-OCT-23 6NDW 1 REMARK REVDAT 4 18-DEC-19 6NDW 1 REMARK REVDAT 3 09-OCT-19 6NDW 1 JRNL REVDAT 2 28-AUG-19 6NDW 1 JRNL REVDAT 1 14-AUG-19 6NDW 0 JRNL AUTH M.J.LYNCH,M.MILLER,M.JAMES,S.ZHANG,K.ZHANG,C.LI,N.W.CHARON, JRNL AUTH 2 B.R.CRANE JRNL TITL STRUCTURE AND CHEMISTRY OF LYSINOALANINE CROSSLINKING IN THE JRNL TITL 2 SPIROCHAETE FLAGELLA HOOK. JRNL REF NAT.CHEM.BIOL. V. 15 959 2019 JRNL REFN ESSN 1552-4469 JRNL PMID 31406373 JRNL DOI 10.1038/S41589-019-0341-3 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 17858 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1786 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 24.8406 - 4.0499 1.00 1271 143 0.1680 0.1760 REMARK 3 2 4.0499 - 3.2167 1.00 1253 138 0.1449 0.1786 REMARK 3 3 3.2167 - 2.8107 1.00 1241 139 0.1585 0.1788 REMARK 3 4 2.8107 - 2.5540 1.00 1242 137 0.1702 0.2028 REMARK 3 5 2.5540 - 2.3711 1.00 1243 138 0.1561 0.1805 REMARK 3 6 2.3711 - 2.2314 1.00 1248 139 0.1592 0.1809 REMARK 3 7 2.2314 - 2.1197 1.00 1242 138 0.1501 0.1901 REMARK 3 8 2.1197 - 2.0275 1.00 1228 137 0.1497 0.1768 REMARK 3 9 2.0275 - 1.9495 1.00 1234 136 0.1523 0.1928 REMARK 3 10 1.9495 - 1.8822 1.00 1222 136 0.1616 0.2026 REMARK 3 11 1.8822 - 1.8234 1.00 1237 138 0.1693 0.2197 REMARK 3 12 1.8234 - 1.7713 1.00 1244 138 0.1721 0.2172 REMARK 3 13 1.7713 - 1.7247 0.94 1167 129 0.1758 0.2330 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.200 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 : 0.006 1363 REMARK 3 ANGLE : 0.775 1862 REMARK 3 CHIRALITY : 0.055 215 REMARK 3 PLANARITY : 0.005 250 REMARK 3 DIHEDRAL : 12.668 803 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 6NDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1000237480. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97700 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17865 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.725 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1WLG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, 2.0M AMMONIUM SULFATE, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.64500 REMARK 290 SMTRY3 2 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: B 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 MET B 0 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 B 400 O HOH B 401 1.73 REMARK 500 O HOH B 364 O HOH B 401 1.82 REMARK 500 O HOH B 422 O HOH B 447 1.98 REMARK 500 O HOH B 362 O HOH B 376 1.98 REMARK 500 O HOH B 397 O HOH B 403 2.07 REMARK 500 O HOH B 205 O HOH B 208 2.09 REMARK 500 O HOH B 334 O HOH B 398 2.13 REMARK 500 O HOH B 258 O HOH B 410 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 325 O HOH B 348 1455 1.99 REMARK 500 O HOH B 364 O HOH B 388 2544 2.17 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 SER B 32 41.05 -102.41 REMARK 500 GLN B 91 -138.94 -100.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 449 DISTANCE = 6.21 ANGSTROMS DBREF 6NDW B 1 177 UNP Q9RQB6 Q9RQB6_TREDN 168 344 SEQADV 6NDW MET B 0 UNP Q9RQB6 INITIATING METHIONINE SEQRES 1 B 178 MET ALA LYS ALA THR THR SER VAL ASN TYR ALA CYS ASN SEQRES 2 B 178 LEU ASP LYS ARG LEU PRO GLU LEU PRO GLU GLY ALA ASN SEQRES 3 B 178 ARG ALA GLN ILE LEU GLU SER THR TRP SER THR GLU PHE SEQRES 4 B 178 LYS VAL TYR ASP SER PHE GLY GLU ALA HIS GLU LEU GLN SEQRES 5 B 178 ILE ASP PHE ALA ARG VAL PRO GLY GLU VAL ASN ALA TRP SEQRES 6 B 178 ARG ALA THR VAL ASN VAL ASP PRO THR ASN ALA ASP ALA SEQRES 7 B 178 THR ALA THR ARG VAL GLY ILE GLY THR THR ASP GLY VAL SEQRES 8 B 178 GLN ASN SER PHE ILE VAL ARG PHE ASP ASN ASN GLY HIS SEQRES 9 B 178 LEU ALA SER VAL THR ASP THR ALA GLY ASN VAL THR SER SEQRES 10 B 178 PRO ALA GLY GLN VAL LEU VAL GLN ILE SER TYR ASN VAL SEQRES 11 B 178 VAL GLY ALA ASN PRO ASP GLU ALA GLY ALA PRO THR ARG SEQRES 12 B 178 HIS THR PHE ASP VAL ASN LEU GLY GLU ILE GLY THR SER SEQRES 13 B 178 LYS ASN THR ILE THR GLN PHE SER ASP LYS SER THR THR SEQRES 14 B 178 LYS ALA TYR GLU GLN ASP GLY TYR THR FORMUL 2 HOH *249(H2 O) HELIX 1 AA1 ASN B 25 SER B 32 1 8 HELIX 2 AA2 ASN B 74 ALA B 79 1 6 SHEET 1 AA1 5 ARG B 81 GLY B 83 0 SHEET 2 AA1 5 GLN B 120 ASN B 128 -1 O GLN B 124 N GLY B 83 SHEET 3 AA1 5 ARG B 142 GLU B 151 -1 O PHE B 145 N ILE B 125 SHEET 4 AA1 5 SER B 6 ASN B 12 1 N VAL B 7 O ASN B 148 SHEET 5 AA1 5 THR B 167 GLN B 173 -1 O GLU B 172 N ASN B 8 SHEET 1 AA2 5 THR B 33 TYR B 41 0 SHEET 2 AA2 5 ALA B 47 ARG B 56 -1 O HIS B 48 N VAL B 40 SHEET 3 AA2 5 ALA B 63 VAL B 70 -1 O ARG B 65 N ALA B 55 SHEET 4 AA2 5 SER B 93 PHE B 98 -1 O PHE B 94 N ALA B 66 SHEET 5 AA2 5 LEU B 104 ASP B 109 -1 O SER B 106 N ARG B 97 CRYST1 33.104 61.290 43.790 90.00 104.45 90.00 P 1 21 1 2 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 0.030208 0.000000 0.007782 0.00000 SCALE2 0.000000 0.016316 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023582 0.00000