PDB Short entry for 5DZO HEADER IMMUNE SYSTEM 25-SEP-15 5DZO TITLE CRYSTAL STRUCTURE OF HUMAN T-CELL IMMUNOGLOBULIN AND MUCIN DOMAIN TITLE 2 PROTEIN 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATITIS A VIRUS CELLULAR RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 22-127; COMPND 5 SYNONYM: HAVCR-1,KIDNEY INJURY MOLECULE 1,KIM-1,T-CELL IMMUNOGLOBULIN COMPND 6 AND MUCIN DOMAIN-CONTAINING PROTEIN 1,TIMD-1,T-CELL IMMUNOGLOBULIN COMPND 7 MUCIN RECEPTOR 1,TIM-1,T-CELL MEMBRANE PROTEIN 1; COMPND 8 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: HAVCR1, KIM1, TIM1, TIMD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RECEPTOR, IG V DOMAIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.YUAN,Z.RAO,X.WANG REVDAT 2 10-FEB-16 5DZO 1 JRNL REVDAT 1 25-NOV-15 5DZO 0 JRNL AUTH S.YUAN,L.CAO,H.LING,M.DANG,Y.SUN,X.ZHANG,Y.CHEN,L.ZHANG, JRNL AUTH 2 D.SU,X.WANG,Z.RAO JRNL TITL TIM-1 ACTS A DUAL-ATTACHMENT RECEPTOR FOR EBOLAVIRUS BY JRNL TITL 2 INTERACTING DIRECTLY WITH VIRAL GP AND THE PS ON THE VIRAL JRNL TITL 3 ENVELOPE. JRNL REF PROTEIN CELL V. 6 814 2015 JRNL REFN ESSN 1674-8018 JRNL PMID 26487564 JRNL DOI 10.1007/S13238-015-0220-Y REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 26993 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 1282 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 33.0147 - 2.7060 1.00 3153 143 0.1583 0.1784 REMARK 3 2 2.7060 - 2.1480 1.00 2961 171 0.1662 0.1877 REMARK 3 3 2.1480 - 1.8765 1.00 2961 121 0.1551 0.1737 REMARK 3 4 1.8765 - 1.7049 1.00 2881 161 0.1549 0.1758 REMARK 3 5 1.7049 - 1.5827 0.99 2860 158 0.1484 0.1478 REMARK 3 6 1.5827 - 1.4894 0.99 2892 128 0.1425 0.1642 REMARK 3 7 1.4894 - 1.4148 0.99 2851 156 0.1511 0.1798 REMARK 3 8 1.4148 - 1.3532 0.97 2802 131 0.1519 0.1774 REMARK 3 9 1.3532 - 1.3011 0.83 2350 113 0.1500 0.1686 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.770 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 : 0.013 859 REMARK 3 ANGLE : 1.411 1164 REMARK 3 CHIRALITY : 0.068 131 REMARK 3 PLANARITY : 0.008 149 REMARK 3 DIHEDRAL : 12.359 306 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 4 THROUGH 32 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.0879 0.4697 10.9214 REMARK 3 T TENSOR REMARK 3 T11: 0.0957 T22: 0.0881 REMARK 3 T33: 0.0996 T12: -0.0107 REMARK 3 T13: -0.0027 T23: -0.0083 REMARK 3 L TENSOR REMARK 3 L11: 0.8591 L22: 0.7730 REMARK 3 L33: 1.8203 L12: -0.0778 REMARK 3 L13: -0.5151 L23: -0.2455 REMARK 3 S TENSOR REMARK 3 S11: 0.0366 S12: -0.0498 S13: 0.0090 REMARK 3 S21: 0.0255 S22: -0.0012 S23: -0.0235 REMARK 3 S31: -0.0779 S32: 0.0480 S33: -0.0354 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 33 THROUGH 42 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.0495 -11.7093 3.7992 REMARK 3 T TENSOR REMARK 3 T11: 0.1637 T22: 0.0928 REMARK 3 T33: 0.1207 T12: 0.0144 REMARK 3 T13: 0.0054 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 3.2987 L22: 0.8319 REMARK 3 L33: 0.1627 L12: -1.4673 REMARK 3 L13: -0.2709 L23: -0.0388 REMARK 3 S TENSOR REMARK 3 S11: -0.0184 S12: 0.0382 S13: -0.2413 REMARK 3 S21: -0.0712 S22: -0.0451 S23: 0.1232 REMARK 3 S31: 0.2773 S32: 0.0576 S33: -0.0107 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 43 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.5827 -1.5061 -0.0393 REMARK 3 T TENSOR REMARK 3 T11: 0.1271 T22: 0.0943 REMARK 3 T33: 0.0750 T12: -0.0037 REMARK 3 T13: 0.0135 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 2.0673 L22: 1.9982 REMARK 3 L33: 0.6115 L12: 0.9603 REMARK 3 L13: -0.5211 L23: -0.8141 REMARK 3 S TENSOR REMARK 3 S11: -0.1033 S12: 0.1183 S13: 0.0171 REMARK 3 S21: -0.2732 S22: 0.0365 S23: -0.0297 REMARK 3 S31: 0.2415 S32: 0.0355 S33: 0.0020 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 48 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.0825 5.1207 -2.6500 REMARK 3 T TENSOR REMARK 3 T11: 0.1524 T22: 0.1090 REMARK 3 T33: 0.1683 T12: -0.0082 REMARK 3 T13: 0.0064 T23: 0.0335 REMARK 3 L TENSOR REMARK 3 L11: 1.7302 L22: 1.0017 REMARK 3 L33: 4.8903 L12: -0.5439 REMARK 3 L13: 1.7140 L23: 0.7202 REMARK 3 S TENSOR REMARK 3 S11: -0.1928 S12: 0.4660 S13: 0.3274 REMARK 3 S21: 0.0133 S22: 0.0049 S23: 0.0575 REMARK 3 S31: -0.5479 S32: 0.1499 S33: 0.1686 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 56 THROUGH 65 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.3662 4.6681 3.5189 REMARK 3 T TENSOR REMARK 3 T11: 0.1062 T22: 0.0739 REMARK 3 T33: 0.0912 T12: 0.0255 REMARK 3 T13: 0.0055 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 7.1130 L22: 2.2924 REMARK 3 L33: 2.8779 L12: 2.7044 REMARK 3 L13: 1.9093 L23: 0.5244 REMARK 3 S TENSOR REMARK 3 S11: -0.0291 S12: -0.0293 S13: 0.2496 REMARK 3 S21: -0.0323 S22: -0.0227 S23: 0.1039 REMARK 3 S31: -0.2115 S32: -0.1051 S33: 0.0033 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 66 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.7432 8.6230 9.1006 REMARK 3 T TENSOR REMARK 3 T11: 0.1531 T22: 0.0924 REMARK 3 T33: 0.1208 T12: -0.0298 REMARK 3 T13: -0.0012 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 6.7501 L22: 8.8848 REMARK 3 L33: 4.1205 L12: 3.7394 REMARK 3 L13: -2.7520 L23: 1.0520 REMARK 3 S TENSOR REMARK 3 S11: 0.1530 S12: -0.1268 S13: 0.1962 REMARK 3 S21: -0.0034 S22: 0.0133 S23: -0.4202 REMARK 3 S31: -0.5369 S32: 0.3095 S33: -0.0100 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 73 THROUGH 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.3477 -2.0530 8.8835 REMARK 3 T TENSOR REMARK 3 T11: 0.0817 T22: 0.0853 REMARK 3 T33: 0.0602 T12: -0.0096 REMARK 3 T13: -0.0019 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 4.2912 L22: 0.8814 REMARK 3 L33: 1.3032 L12: 0.1104 REMARK 3 L13: -0.6189 L23: -0.2827 REMARK 3 S TENSOR REMARK 3 S11: 0.0101 S12: -0.0197 S13: 0.0288 REMARK 3 S21: -0.0135 S22: 0.0207 S23: 0.0683 REMARK 3 S31: -0.0038 S32: -0.1425 S33: -0.0208 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 91 THROUGH 98 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.7270 -7.0856 3.7242 REMARK 3 T TENSOR REMARK 3 T11: 0.1256 T22: 0.1728 REMARK 3 T33: 0.1530 T12: 0.0165 REMARK 3 T13: -0.0144 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 3.4603 L22: 1.1570 REMARK 3 L33: 4.5568 L12: -1.9910 REMARK 3 L13: -0.2280 L23: 0.3591 REMARK 3 S TENSOR REMARK 3 S11: -0.0254 S12: 0.0482 S13: 0.4838 REMARK 3 S21: 0.0120 S22: 0.1237 S23: -0.4965 REMARK 3 S31: 0.1796 S32: 0.2718 S33: -0.1077 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 99 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4783 -4.6729 14.7132 REMARK 3 T TENSOR REMARK 3 T11: 0.1106 T22: 0.1098 REMARK 3 T33: 0.0852 T12: -0.0000 REMARK 3 T13: 0.0013 T23: 0.0014 REMARK 3 L TENSOR REMARK 3 L11: 2.0075 L22: 1.5652 REMARK 3 L33: 3.2599 L12: 0.1831 REMARK 3 L13: -2.5365 L23: -0.3362 REMARK 3 S TENSOR REMARK 3 S11: -0.0197 S12: -0.2220 S13: -0.1927 REMARK 3 S21: 0.0597 S22: 0.0299 S23: 0.1288 REMARK 3 S31: 0.0846 S32: -0.0314 S33: -0.0767 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 5DZO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214080. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27042 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 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 (%) : 97.4 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.4000 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) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.17300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M SODIUM NITRATE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 42.08100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.36950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.36950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 63.12150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.36950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.36950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.04050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.36950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.36950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 63.12150 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.36950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.36950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.04050 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.08100 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 OD1 ASN A 97 O HOH A 301 1.82 REMARK 500 O HOH A 433 O HOH A 452 2.03 REMARK 500 O HOH A 304 O HOH A 381 2.04 REMARK 500 NZ LYS A 56 O HOH A 302 2.18 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 CD GLU A 10 OE2 GLU A 10 8555 0.38 REMARK 500 OE2 GLU A 10 OE2 GLU A 10 8555 0.87 REMARK 500 OE1 GLU A 10 OE2 GLU A 10 8555 1.40 REMARK 500 CD GLU A 10 CD GLU A 10 8555 1.59 REMARK 500 CG GLU A 10 OE2 GLU A 10 8555 1.80 REMARK 500 O HOH A 315 O HOH A 399 8555 1.87 REMARK 500 O HOH A 415 O HOH A 440 6455 1.88 REMARK 500 O HOH A 395 O HOH A 429 4555 1.96 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 CYS A 40 74.90 25.45 REMARK 500 ASN A 42 54.84 -118.62 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 456 DISTANCE = 6.49 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 203 DBREF 5DZO A 5 110 UNP Q96D42 HAVR1_HUMAN 22 127 SEQADV 5DZO MET A 4 UNP Q96D42 INITIATING METHIONINE SEQRES 1 A 107 MET VAL LYS VAL GLY GLY GLU ALA GLY PRO SER VAL THR SEQRES 2 A 107 LEU PRO CYS HIS TYR SER GLY ALA VAL THR SER MET CYS SEQRES 3 A 107 TRP ASN ARG GLY SER CYS SER LEU PHE THR CYS GLN ASN SEQRES 4 A 107 GLY ILE VAL TRP THR ASN GLY THR HIS VAL THR TYR ARG SEQRES 5 A 107 LYS ASP THR ARG TYR LYS LEU LEU GLY ASP LEU SER ARG SEQRES 6 A 107 ARG ASP VAL SER LEU THR ILE GLU ASN THR ALA VAL SER SEQRES 7 A 107 ASP SER GLY VAL TYR CYS CYS ARG VAL GLU HIS ARG GLY SEQRES 8 A 107 TRP PHE ASN ASP MET LYS ILE THR VAL SER LEU GLU ILE SEQRES 9 A 107 VAL PRO PRO HET NO3 A 201 4 HET NO3 A 202 4 HET NA A 203 1 HETNAM NO3 NITRATE ION HETNAM NA SODIUM ION FORMUL 2 NO3 2(N O3 1-) FORMUL 4 NA NA 1+ FORMUL 5 HOH *156(H2 O) HELIX 1 AA1 ASP A 65 ARG A 69 5 5 HELIX 2 AA2 ALA A 79 SER A 83 5 5 SHEET 1 AA1 6 VAL A 5 GLU A 10 0 SHEET 2 AA1 6 MET A 99 VAL A 108 1 O SER A 104 N VAL A 5 SHEET 3 AA1 6 GLY A 84 VAL A 90 -1 N TYR A 86 O VAL A 103 SHEET 4 AA1 6 MET A 28 ARG A 32 -1 N CYS A 29 O ARG A 89 SHEET 5 AA1 6 GLY A 43 THR A 47 -1 O ILE A 44 N TRP A 30 SHEET 6 AA1 6 VAL A 52 ARG A 55 -1 O THR A 53 N TRP A 46 SHEET 1 AA2 3 VAL A 15 LEU A 17 0 SHEET 2 AA2 3 LEU A 73 ILE A 75 -1 O LEU A 73 N LEU A 17 SHEET 3 AA2 3 TYR A 60 LYS A 61 -1 N LYS A 61 O THR A 74 SSBOND 1 CYS A 19 CYS A 88 1555 1555 2.02 SSBOND 2 CYS A 29 CYS A 40 1555 1555 2.04 SSBOND 3 CYS A 35 CYS A 87 1555 1555 2.04 SITE 1 AC1 9 ASN A 31 SER A 34 CYS A 35 SER A 36 SITE 2 AC1 9 PHE A 38 CYS A 40 CYS A 87 ARG A 89 SITE 3 AC1 9 HOH A 360 SITE 1 AC2 6 VAL A 85 GLY A 94 TRP A 95 PHE A 96 SITE 2 AC2 6 ASN A 97 HOH A 311 SITE 1 AC3 2 SER A 22 HIS A 92 CRYST1 50.739 50.739 84.162 90.00 90.00 90.00 P 43 21 2 8 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 0.019709 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019709 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011882 0.00000