HEADER MOTOR PROTEIN 14-DEC-18 6NDT TITLE DEHYDROALANINE INTERMEDIATE OF THE FLGE D2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAGELLAR HOOK PROTEIN FLGE; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DEHYDROALANINE IN POSITION 11, N-TERMINAL METHIONINE COMPND 6 MISSING 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, DEHYDROALANINE, MOTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.J.LYNCH,B.R.CRANE REVDAT 4 18-DEC-19 6NDT 1 REMARK REVDAT 3 09-OCT-19 6NDT 1 JRNL REVDAT 2 28-AUG-19 6NDT 1 JRNL REVDAT 1 14-AUG-19 6NDT 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. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 34275 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.840 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 49.5029 - 3.4322 0.98 2497 154 0.1658 0.1640 REMARK 3 2 3.4322 - 2.7243 0.99 2404 150 0.1767 0.1916 REMARK 3 3 2.7243 - 2.3799 0.98 2358 146 0.1727 0.1922 REMARK 3 4 2.3799 - 2.1623 0.99 2359 146 0.1644 0.1752 REMARK 3 5 2.1623 - 2.0073 0.98 2343 146 0.1626 0.1776 REMARK 3 6 2.0073 - 1.8890 0.98 2325 143 0.1720 0.1939 REMARK 3 7 1.8890 - 1.7944 0.98 2301 142 0.1776 0.1851 REMARK 3 8 1.7944 - 1.7163 0.98 2320 144 0.1824 0.2221 REMARK 3 9 1.7163 - 1.6502 0.98 2315 143 0.1856 0.2121 REMARK 3 10 1.6502 - 1.5932 0.98 2282 142 0.1803 0.2190 REMARK 3 11 1.5932 - 1.5434 0.98 2297 143 0.1809 0.1971 REMARK 3 12 1.5434 - 1.4993 0.96 2255 140 0.1846 0.1899 REMARK 3 13 1.4993 - 1.4598 0.95 2225 138 0.1985 0.1868 REMARK 3 14 1.4598 - 1.4242 0.86 1994 123 0.2369 0.2638 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.57 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 : 0.010 1362 REMARK 3 ANGLE : 1.106 1861 REMARK 3 CHIRALITY : 0.097 214 REMARK 3 PLANARITY : 0.008 251 REMARK 3 DIHEDRAL : 20.787 477 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 6NDT 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_1000237494. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10500 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34285 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M SODIUM CITRATE TRIBASIC, PH 8.2, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 19.24400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.47300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.17200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.47300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.24400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.17200 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: 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 C DHA B 11 H ASN B 12 1.22 REMARK 500 O GLY B 138 O HOH B 201 2.18 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 ASP B 71 73.13 56.00 REMARK 500 GLN B 91 -153.05 -97.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 26 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 6NDT B 1 177 UNP Q9RQB6 Q9RQB6_TREDN 168 344 SEQADV 6NDT MET B 0 UNP Q9RQB6 INITIATING METHIONINE SEQADV 6NDT DHA B 11 UNP Q9RQB6 CYS 178 CONFLICT SEQRES 1 B 178 MET ALA LYS ALA THR THR SER VAL ASN TYR ALA DHA 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 HET DHA B 11 5 HETNAM DHA 2-AMINO-ACRYLIC ACID HETSYN DHA 2,3-DIDEHYDROALANINE FORMUL 1 DHA C3 H5 N O2 FORMUL 2 HOH *187(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 ILE B 159 THR B 160 1 O THR B 160 N DHA B 11 SHEET 1 AA2 5 ARG B 81 GLY B 83 0 SHEET 2 AA2 5 GLN B 120 ASN B 128 -1 O GLN B 124 N GLY B 83 SHEET 3 AA2 5 ARG B 142 GLU B 151 -1 O PHE B 145 N ILE B 125 SHEET 4 AA2 5 SER B 6 ASN B 12 1 N VAL B 7 O ASN B 148 SHEET 5 AA2 5 LYS B 169 GLN B 173 -1 O TYR B 171 N ASN B 8 SHEET 1 AA3 5 TRP B 34 TYR B 41 0 SHEET 2 AA3 5 ALA B 47 ARG B 56 -1 O LEU B 50 N PHE B 38 SHEET 3 AA3 5 ALA B 63 VAL B 70 -1 O ARG B 65 N ALA B 55 SHEET 4 AA3 5 SER B 93 PHE B 98 -1 O PHE B 94 N ALA B 66 SHEET 5 AA3 5 LEU B 104 ASP B 109 -1 O ALA B 105 N ARG B 97 LINK C ALA B 10 N DHA B 11 1555 1555 1.32 LINK C DHA B 11 N ASN B 12 1555 1555 1.22 CRYST1 38.488 48.344 98.946 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 0.025982 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020685 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010107 0.00000