PDB Short entry for 1D3L HEADER CELL ADHESION 29-SEP-99 1D3L TITLE D1D2-ICAM-1 FULLY GLYCOSYLATED, VARIATION OF D1-D2 INTERDOMAIN ANGLE TITLE 2 IN DIFFERENT CRYSTAL STRUCTURES. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (INTERCELLULAR ADHESION MOLECULE-1); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FIRST TWO DOMAINS, RESIDUES 1-185; COMPND 5 SYNONYM: ICAM-1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS RHINOVIRUS RECEPTOR, ADHESION PROTEIN, GLYCOPROTEIN, IMMUNOGLOBULIN KEYWDS 2 FOLD, CELL ADHESION EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR J.BELLA,P.R.KOLATKAR,M.G.ROSSMANN REVDAT 4 09-AUG-23 1D3L 1 REMARK REVDAT 3 24-FEB-09 1D3L 1 VERSN REVDAT 2 01-APR-03 1D3L 1 JRNL REVDAT 1 01-DEC-99 1D3L 0 JRNL AUTH P.R.KOLATKAR,J.BELLA,N.H.OLSON,C.M.BATOR,T.S.BAKER, JRNL AUTH 2 M.G.ROSSMANN JRNL TITL STRUCTURAL STUDIES OF TWO RHINOVIRUS SEROTYPES COMPLEXED JRNL TITL 2 WITH FRAGMENTS OF THEIR CELLULAR RECEPTOR. JRNL REF EMBO J. V. 18 6249 1999 JRNL REFN ISSN 0261-4189 JRNL PMID 10562537 JRNL DOI 10.1093/EMBOJ/18.22.6249 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.BELLA,P.R.KOLATKAR,C.W.MARLOR,J.M.GREVE,M.G.ROSSMANN REMARK 1 TITL THE STRUCTURE OF THE TWO AMINO-TERMINAL DOMAINS OF HUMAN REMARK 1 TITL 2 ICAM-1 SUGGESTS HOW IT FUNCTIONS AS A RHINOVIRUS RECEPTOR REMARK 1 TITL 3 AND AS AN LFA-1 INTEGRIN LIGAND. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 95 4140 1998 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.95.8.4140 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.M.CASASNOVAS,T.STEHLE,J.H.LIU,J.H.WANG,T.A.SPRINGER REMARK 1 TITL A DIMERIC CRYSTAL STRUCTURE FOR THE N-TERMINAL TWO DOMAINS REMARK 1 TITL 2 OF INTERCELLULAR ADHESION MOLECULE-1 REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 95 4134 1998 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.95.8.4134 REMARK 1 REFERENCE 3 REMARK 1 AUTH P.R.KOLATKAR,M.A.OLIVEIRA,M.G.ROSSMANN,A.H.ROBBINS,S.KATTI, REMARK 1 AUTH 2 H.HOOVER-LITTY,C.FORTE,J.M.GREVE,A.MCCLELLAND,N.H.OLSON REMARK 1 TITL PRELIMINARY X-RAY CRYSTALLOGRAPHIC ANALYSIS OF INTERCELLULAR REMARK 1 TITL 2 ADHESION MOLECULE-1 REMARK 1 REF J.MOL.BIOL. V. 225 1127 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 3.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 3841 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.371 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 185 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.89 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: COORDINATES AFTER RIGID-BODY REFINEMENT REMARK 4 REMARK 4 1D3L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1000009760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4634 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.816 REMARK 200 RESOLUTION RANGE LOW (A) : 26.582 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 72.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 21.8 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 <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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1IAM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS DESIALATED WITH REMARK 280 NEURAMINIDASE (8 HR AT 37 DEGREES IN 100 MM SODIUM ACETATE, PH REMARK 280 6.5, 10 MG/ML PROTEIN, 0.1 ENZYME UNIT/ML), DIALYZED AGAINST 10 REMARK 280 MM TRIS, 25 MM NACL (PH 6.0), AND PASSED THROUGH MONO-Q COLUMN. REMARK 280 DESIALATED MATERIAL WAS CRYSTALLIZED BY HANGING DROP METHODS: 17 REMARK 280 MG/ML PROTEIN IN BUFFER: 10 MM TRIS,25 MM NACL,1 MM MGCL2,1 MM REMARK 280 CACL2, WAS PRECIPITATED FROM 24-27% PEG 3350 IN SAME BUFFER. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.59000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 97.18000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 97.18000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 48.59000 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: GS1 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: N-GLYCOSYLATION SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: GS2 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: N-GLYCOSYLATION SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: GS3 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: N-GLYCOSYLATION SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: GS4 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: N-GLYCOSYLATION SITE DBREF 1D3L A 1 185 UNP P05362 ICAM1_HUMAN 28 212 SEQRES 1 A 185 GLN THR SER VAL SER PRO SER LYS VAL ILE LEU PRO ARG SEQRES 2 A 185 GLY GLY SER VAL LEU VAL THR CYS SER THR SER CYS ASP SEQRES 3 A 185 GLN PRO LYS LEU LEU GLY ILE GLU THR PRO LEU PRO LYS SEQRES 4 A 185 LYS GLU LEU LEU LEU PRO GLY ASN ASN ARG LYS VAL TYR SEQRES 5 A 185 GLU LEU SER ASN VAL GLN GLU ASP SER GLN PRO MET CYS SEQRES 6 A 185 TYR SER ASN CYS PRO ASP GLY GLN SER THR ALA LYS THR SEQRES 7 A 185 PHE LEU THR VAL TYR TRP THR PRO GLU ARG VAL GLU LEU SEQRES 8 A 185 ALA PRO LEU PRO SER TRP GLN PRO VAL GLY LYS ASN LEU SEQRES 9 A 185 THR LEU ARG CYS GLN VAL GLU GLY GLY ALA PRO ARG ALA SEQRES 10 A 185 ASN LEU THR VAL VAL LEU LEU ARG GLY GLU LYS GLU LEU SEQRES 11 A 185 LYS ARG GLU PRO ALA VAL GLY GLU PRO ALA GLU VAL THR SEQRES 12 A 185 THR THR VAL LEU VAL ARG ARG ASP HIS HIS GLY ALA ASN SEQRES 13 A 185 PHE SER CYS ARG THR GLU LEU ASP LEU ARG PRO GLN GLY SEQRES 14 A 185 LEU GLU LEU PHE GLU ASN THR SER ALA PRO TYR GLN LEU SEQRES 15 A 185 GLN THR PHE HELIX 1 1 ARG A 116 ASN A 118 5 3 HELIX 2 2 ARG A 166 GLN A 168 5 3 SHEET 1 A 4 THR A 2 SER A 5 0 SHEET 2 A 4 VAL A 17 THR A 23 -1 SHEET 3 A 4 ARG A 49 SER A 55 -1 SHEET 4 A 4 PRO A 38 LEU A 42 -1 SHEET 1 B 2 LYS A 8 PRO A 12 0 SHEET 2 B 2 PHE A 79 TYR A 83 1 SHEET 1 C 3 LEU A 30 GLU A 34 0 SHEET 2 C 3 MET A 64 ASN A 68 -1 SHEET 3 C 3 GLN A 73 LYS A 77 -1 SHEET 1 D 3 ARG A 88 LEU A 91 0 SHEET 2 D 3 ASN A 103 GLU A 111 -1 SHEET 3 D 3 ALA A 140 LEU A 147 -1 SHEET 1 E 4 LEU A 172 THR A 176 0 SHEET 2 E 4 PHE A 157 ASP A 164 -1 SHEET 3 E 4 LEU A 119 ARG A 125 -1 SHEET 4 E 4 LYS A 128 PRO A 134 -1 SITE 1 GS1 1 ASN A 103 SITE 1 GS2 1 ASN A 118 SITE 1 GS3 1 ASN A 156 SITE 1 GS4 1 ASN A 175 CRYST1 54.070 54.070 145.770 90.00 90.00 120.00 P 31 2 1 6 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 0.018495 0.010678 0.000000 0.00000 SCALE2 0.000000 0.021356 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006860 0.00000