HEADER IMMUNE SYSTEM 06-JUN-02 1LY2 TITLE CRYSTAL STRUCTURE OF UNLIGANDED HUMAN CD21 SCR1-SCR2 (COMPLEMENT TITLE 2 RECEPTOR TYPE 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT RECEPTOR TYPE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CD21; EPSTEIN-BARR VIRUS RECEPTOR; COMPND 5 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: CR2; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: X-33; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PICZA (INVITROGEN) SECRETED PROTEIN KEYWDS COMPLEMENT RECEPTOR; EPSTEIN BARR VIRUS; REGULATOR OF COMPLEMENT KEYWDS 2 ACTIVATION; SHORT CONSENSUS REPEAT; VIRAL RECEPTOR; COMPLEMENT KEYWDS 3 CONTROL PROTEIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.E.PROTA,D.R.SAGE,T.STEHLE,J.D.FINGEROTH REVDAT 5 29-JUL-20 1LY2 1 COMPND REMARK SEQADV HETNAM REVDAT 5 2 1 LINK SITE REVDAT 4 13-JUL-11 1LY2 1 VERSN REVDAT 3 24-FEB-09 1LY2 1 VERSN REVDAT 2 23-AUG-02 1LY2 1 JRNL AUTHOR REVDAT 1 05-JUL-02 1LY2 0 JRNL AUTH A.E.PROTA,D.R.SAGE,T.STEHLE,J.D.FINGEROTH JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN CD21: IMPLICATIONS FOR JRNL TITL 2 EPSTEIN-BARR VIRUS AND C3D BINDING. JRNL REF PROC.NATL.ACAD.SCI.USA V. 99 10641 2002 JRNL REFN ISSN 0027-8424 JRNL PMID 12122212 JRNL DOI 10.1073/PNAS.162360499 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11265 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1127 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 : 996 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 146 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 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.340 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: NULL REMARK 4 REMARK 4 1LY2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016398. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.05 REMARK 200 MONOCHROMATOR : WIGGLER REMARK 200 OPTICS : WIGGLER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11265 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 55.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.10000 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: AMORE REMARK 200 STARTING MODEL: CRYSTAL STRUCTURE OF LIGANDED CD21 (COMPLEX WITH REMARK 200 C3D) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP AT 298K, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 DBREF 1LY2 A 0 129 UNP P20023 CR2_HUMAN 20 149 SEQADV 1LY2 GLU A 0 UNP P20023 GLY 20 CLONING ARTIFACT SEQADV 1LY2 ALA A 1 UNP P20023 ILE 21 CLONING ARTIFACT SEQADV 1LY2 ILE A 129 UNP P20023 VAL 149 CLONING ARTIFACT SEQRES 1 A 130 GLU ALA SER CYS GLY SER PRO PRO PRO ILE LEU ASN GLY SEQRES 2 A 130 ARG ILE SER TYR TYR SER THR PRO ILE ALA VAL GLY THR SEQRES 3 A 130 VAL ILE ARG TYR SER CYS SER GLY THR PHE ARG LEU ILE SEQRES 4 A 130 GLY GLU LYS SER LEU LEU CYS ILE THR LYS ASP LYS VAL SEQRES 5 A 130 ASP GLY THR TRP ASP LYS PRO ALA PRO LYS CYS GLU TYR SEQRES 6 A 130 PHE ASN LYS TYR SER SER CYS PRO GLU PRO ILE VAL PRO SEQRES 7 A 130 GLY GLY TYR LYS ILE ARG GLY SER THR PRO TYR ARG HIS SEQRES 8 A 130 GLY ASP SER VAL THR PHE ALA CYS LYS THR ASN PHE SER SEQRES 9 A 130 MET ASN GLY ASN LYS SER VAL TRP CYS GLN ALA ASN ASN SEQRES 10 A 130 MET TRP GLY PRO THR ARG LEU PRO THR CYS VAL SER ILE MODRES 1LY2 ASN A 101 ASN GLYCOSYLATION SITE MODRES 1LY2 ASN A 107 ASN GLYCOSYLATION SITE HET NAG A1001 14 HET NAG A1002 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 4 HOH *146(H2 O) SHEET 1 A 2 SER A 2 CYS A 3 0 SHEET 2 A 2 ILE A 21 ALA A 22 -1 O ILE A 21 N CYS A 3 SHEET 1 B 4 GLY A 12 ILE A 14 0 SHEET 2 B 4 VAL A 26 CYS A 31 -1 O SER A 30 N ARG A 13 SHEET 3 B 4 SER A 42 ILE A 46 -1 O LEU A 43 N ILE A 27 SHEET 4 B 4 THR A 54 TRP A 55 -1 O THR A 54 N ILE A 46 SHEET 1 C 2 PHE A 35 ILE A 38 0 SHEET 2 C 2 LYS A 61 TYR A 64 -1 O LYS A 61 N ILE A 38 SHEET 1 D 2 SER A 70 CYS A 71 0 SHEET 2 D 2 TYR A 88 ARG A 89 -1 O TYR A 88 N CYS A 71 SHEET 1 E 4 GLY A 79 ARG A 83 0 SHEET 2 E 4 SER A 93 CYS A 98 -1 O ALA A 97 N TYR A 80 SHEET 3 E 4 SER A 109 CYS A 112 -1 O VAL A 110 N VAL A 94 SHEET 4 E 4 TRP A 118 GLY A 119 -1 O GLY A 119 N TRP A 111 SHEET 1 F 2 PHE A 102 ASN A 105 0 SHEET 2 F 2 THR A 125 SER A 128 -1 O VAL A 127 N SER A 103 SSBOND 1 CYS A 3 CYS A 45 1555 1555 2.04 SSBOND 2 CYS A 31 CYS A 62 1555 1555 2.04 SSBOND 3 CYS A 71 CYS A 112 1555 1555 2.05 SSBOND 4 CYS A 98 CYS A 126 1555 1555 2.05 LINK ND2 ASN A 101 C1 NAG A1001 1555 1555 1.46 LINK ND2 ASN A 107 C1 NAG A1002 1555 1555 1.46 CISPEP 1 THR A 19 PRO A 20 0 -0.16 CISPEP 2 THR A 86 PRO A 87 0 -0.22 CISPEP 3 GLY A 119 PRO A 120 0 0.15 CRYST1 31.600 33.270 42.110 91.51 111.44 117.81 P 1 1 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 0.031646 0.016692 0.016910 0.00000 SCALE2 0.000000 0.033982 0.008369 0.00000 SCALE3 0.000000 0.000000 0.026275 0.00000