HEADER IMMUNE SYSTEM 07-DEC-15 5F70 TITLE CRYSTAL STRUCTURES OF HUMAN TIM MEMBERS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATITIS A VIRUS CELLULAR RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 21-123; COMPND 5 SYNONYM: HAVCR-1, T-CELL IMMUNOGLOBULIN AND MUCIN DOMAIN-CONTAINING COMPND 6 PROTEIN 1, TIMD-1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TIMD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HTIM, EBOLA VIRUS, RECEPTOR, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR G.F.GAO,G.LU,H.WANG,J.QI REVDAT 2 08-NOV-23 5F70 1 JRNL REMARK REVDAT 1 03-FEB-16 5F70 0 JRNL AUTH H.WANG,J.X.QI,N.N.LIU JRNL TITL CRYSTAL STRUCTURES OF HUMAN TIM MEMBERS: EBOLAVIRUS JRNL TITL 2 ENTRY-ENHANCING RECEPTORS JRNL REF CHIN.SCI.BULL. V. 60 3438 2015 JRNL REFN ISSN 1001-6538 JRNL DOI 10.1360/N972015-01255 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 7932 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 366 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 26.4690 - 2.5917 0.97 2581 127 0.1937 0.2354 REMARK 3 2 2.5917 - 2.0574 0.99 2536 125 0.1889 0.3067 REMARK 3 3 2.0574 - 1.7974 0.98 2449 114 0.2265 0.2805 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 48.04 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.990 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) : -8.82700 REMARK 3 B22 (A**2) : 8.77600 REMARK 3 B33 (A**2) : 0.05100 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 : 0.007 814 REMARK 3 ANGLE : 1.188 1100 REMARK 3 CHIRALITY : 0.090 124 REMARK 3 PLANARITY : 0.005 139 REMARK 3 DIHEDRAL : 14.538 287 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 3.0066 -0.6822 -11.0791 REMARK 3 T TENSOR REMARK 3 T11: 0.1740 T22: 0.1687 REMARK 3 T33: 0.1767 T12: 0.0045 REMARK 3 T13: 0.0088 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.5008 L22: 0.4511 REMARK 3 L33: 0.6575 L12: -0.0039 REMARK 3 L13: 0.1578 L23: 0.0023 REMARK 3 S TENSOR REMARK 3 S11: -0.0186 S12: 0.0172 S13: -0.0442 REMARK 3 S21: 0.0638 S22: 0.0036 S23: 0.0304 REMARK 3 S31: -0.0182 S32: -0.0126 S33: 0.0000 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 5F70 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97972 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7934 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 97.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : 0.10500 REMARK 200 FOR THE DATA SET : 11.0920 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.46900 REMARK 200 R SYM FOR SHELL (I) : 0.46900 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2OR8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE. 20%(V/V) JEFFAMINE ED REMARK 280 -2001 (PH 7.0), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 13.89350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.43750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.88650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.43750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.89350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.88650 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 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 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 257 O HOH A 277 2.12 REMARK 500 O HOH A 253 O HOH A 279 2.16 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 THR A 37 -162.54 -168.31 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 A 286 DISTANCE = 6.01 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5F71 RELATED DB: PDB DBREF 5F70 A 2 104 UNP Q96D42 HAVR1_HUMAN 21 123 SEQRES 1 A 103 SER VAL LYS VAL GLY GLY GLU ALA GLY PRO SER VAL THR SEQRES 2 A 103 LEU PRO CYS HIS TYR SER GLY ALA VAL THR SER MET CYS SEQRES 3 A 103 TRP ASN ARG GLY SER CYS SER LEU PHE THR CYS GLN ASN SEQRES 4 A 103 GLY ILE VAL TRP THR ASN GLY THR HIS VAL THR TYR ARG SEQRES 5 A 103 LYS ASP THR ARG TYR LYS LEU LEU GLY ASP LEU SER ARG SEQRES 6 A 103 ARG ASP VAL SER LEU THR ILE GLU ASN THR ALA VAL SER SEQRES 7 A 103 ASP SER GLY VAL TYR CYS CYS ARG VAL GLU HIS ARG GLY SEQRES 8 A 103 TRP PHE ASN ASP MET LYS ILE THR VAL SER LEU GLU FORMUL 2 HOH *86(H2 O) HELIX 1 AA1 ASP A 63 ARG A 67 5 5 HELIX 2 AA2 ALA A 77 SER A 81 5 5 SHEET 1 AA1 6 VAL A 3 GLY A 7 0 SHEET 2 AA1 6 PHE A 94 LEU A 103 1 O THR A 100 N VAL A 5 SHEET 3 AA1 6 GLY A 82 GLU A 89 -1 N VAL A 88 O ASN A 95 SHEET 4 AA1 6 MET A 26 ARG A 30 -1 N CYS A 27 O ARG A 87 SHEET 5 AA1 6 GLY A 41 ASN A 46 -1 O ILE A 42 N TRP A 28 SHEET 6 AA1 6 HIS A 49 ARG A 53 -1 O HIS A 49 N ASN A 46 SHEET 1 AA2 3 VAL A 13 LEU A 15 0 SHEET 2 AA2 3 LEU A 71 ILE A 73 -1 O LEU A 71 N LEU A 15 SHEET 3 AA2 3 TYR A 58 LYS A 59 -1 N LYS A 59 O THR A 72 SSBOND 1 CYS A 17 CYS A 86 1555 1555 2.04 SSBOND 2 CYS A 27 CYS A 38 1555 1555 2.04 SSBOND 3 CYS A 33 CYS A 85 1555 1555 2.05 CRYST1 27.787 33.773 86.875 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 0.035988 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029609 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011511 0.00000