HEADER IMMUNOGLOBULIN 13-JUL-96 1HCV TITLE LLAMA HEAVY CHAIN VARIABLE DOMAIN AGAINST ALPHA SUBUNIT OF HCG (HUMAN TITLE 2 CHORIONIC GONADOTROPIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN G; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HEAVY CHAIN VARIABLE DOMAIN FROM LLAMA; COMPND 5 SYNONYM: HC-V LLAMA; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: FROM IMMUNIZED LLAMA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_COMMON: LLAMA; SOURCE 4 ORGANISM_TAXID: 9844; SOURCE 5 TISSUE: BLOOD; SOURCE 6 CELL: LYMPHOCYTE; SOURCE 7 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 8 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS CAMELIDS, IMMUNOGLOBULIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SPINELLI,C.CAMBILLAU,M.TEGONI REVDAT 5 09-OCT-24 1HCV 1 REMARK REVDAT 4 03-APR-24 1HCV 1 REMARK REVDAT 3 24-FEB-09 1HCV 1 VERSN REVDAT 2 01-APR-03 1HCV 1 JRNL REVDAT 1 23-JUL-97 1HCV 0 JRNL AUTH S.SPINELLI,L.FRENKEN,D.BOURGEOIS,L.DE RON,W.BOS,T.VERRIPS, JRNL AUTH 2 C.ANGUILLE,C.CAMBILLAU,M.TEGONI JRNL TITL THE CRYSTAL STRUCTURE OF A LLAMA HEAVY CHAIN VARIABLE JRNL TITL 2 DOMAIN. JRNL REF NAT.STRUCT.BIOL. V. 3 752 1996 JRNL REFN ISSN 1072-8368 JRNL PMID 8784347 JRNL DOI 10.1038/NSB0996-752 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.DESMYTER,T.R.TRANSUE,M.A.GHAHROUDI,M.H.THI,F.POORTMANS, REMARK 1 AUTH 2 R.HAMERS,S.MUYLDERMANS,L.WYNS REMARK 1 TITL CRYSTAL STRUCTURE OF A CAMEL SINGLE-DOMAIN VH ANTIBODY REMARK 1 TITL 2 FRAGMENT IN COMPLEX WITH LYSOZYME REMARK 1 REF NAT.STRUCT.BIOL. V. 3 803 1996 REMARK 1 REFN ISSN 1072-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.SHERIFF,K.L.CONSTANTINE REMARK 1 TITL REDEFINING THE MINIMAL ANTIGEN-BINDING FRAGMENT REMARK 1 REF NAT.STRUCT.BIOL. V. 3 733 1996 REMARK 1 REFN ISSN 1072-8368 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.MUYLDERMANS,T.ATARHOUCH,J.SALDANHA,J.A.BARBOSA,R.HAMERS REMARK 1 TITL SEQUENCE AND STRUCTURE OF VH DOMAIN FROM NATURALLY OCCURRING REMARK 1 TITL 2 CAMEL HEAVY CHAIN IMMUNOGLOBULINS LACKING LIGHT CHAINS REMARK 1 REF PROTEIN ENG. V. 7 1129 1994 REMARK 1 REFN ISSN 0269-2139 REMARK 1 REFERENCE 4 REMARK 1 AUTH C.HAMERS-CASTERMAN,T.ATARHOUCH,S.MUYLDERMANS,G.ROBINSON, REMARK 1 AUTH 2 C.HAMERS,E.B.SONGA,N.BENDAHMAN,R.HAMERS REMARK 1 TITL NATURALLY OCCURRING ANTIBODIES DEVOID OF LIGHT CHAINS REMARK 1 REF NATURE V. 363 446 1993 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 7950 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : YES REMARK 3 FREE R VALUE TEST SET SELECTION : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 844 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 : 859 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 103 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.00 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.200 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 1HCV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173786. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-96 REMARK 200 TEMPERATURE (KELVIN) : 290 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-D REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4270 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 1.600 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: VH OF FAB FRAGMENT OF ANTIBODY AGAINST 2-PHENYL REMARK 200 -OXAZOLONE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, PEG 8K 25%, TRIS REMARK 280 0.1M, PH 8.0, VAPOR DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 20.91500 REMARK 290 SMTRY3 2 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 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 ASP A 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 27 CB CG CD NE CZ NH1 NH2 REMARK 470 SER A 30 CB OG REMARK 470 THR A 31 OG1 CG2 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 HD22 ASN A 52 H SER A 54 1.33 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 HH11 ARG A 19 HG SER A 113 2555 1.20 REMARK 500 HE1 TRP A 103 H2 HOH A 165 2646 1.31 REMARK 500 H ARG A 19 H2 HOH A 121 1455 1.34 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 ARG A 27 94.77 84.63 REMARK 500 REMARK 500 REMARK: NULL DBREF 1HCV A 2 113 EMBL AJ236094 CAA15406 2 117 SEQRES 1 A 117 ASP VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 117 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 117 ARG THR GLY SER THR TYR ASP MET GLY TRP PHE ARG GLN SEQRES 4 A 117 ALA PRO GLY LYS GLU ARG GLU SER VAL ALA ALA ILE ASN SEQRES 5 A 117 TRP ASP SER ALA ARG THR TYR TYR ALA SER SER VAL ARG SEQRES 6 A 117 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS LYS THR SEQRES 7 A 117 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 A 117 ALA VAL TYR THR CYS GLY ALA GLY GLU GLY GLY THR TRP SEQRES 9 A 117 ASP SER TRP GLY GLN GLY THR GLN VAL THR VAL SER SER FORMUL 2 HOH *103(H2 O) HELIX 1 1 PRO A 84 ASP A 86 5 3 SHEET 1 A 4 LEU A 4 SER A 7 0 SHEET 2 A 4 LEU A 18 ALA A 24 -1 N ALA A 23 O GLN A 5 SHEET 3 A 4 THR A 77 MET A 82 -1 N MET A 82 O LEU A 18 SHEET 4 A 4 PHE A 67 ASP A 72 -1 N ASP A 72 O THR A 77 SHEET 1 B 6 GLY A 10 GLN A 13 0 SHEET 2 B 6 THR A 107 SER A 112 1 N THR A 110 O GLY A 10 SHEET 3 B 6 ALA A 88 GLU A 96 -1 N TYR A 90 O THR A 107 SHEET 4 B 6 TYR A 32 GLN A 39 -1 N GLN A 39 O VAL A 89 SHEET 5 B 6 GLU A 46 ASN A 52 -1 N ILE A 51 O MET A 34 SHEET 6 B 6 THR A 57 TYR A 59 -1 N TYR A 58 O ALA A 50 SHEET 1 C 2 GLY A 93 GLU A 96 0 SHEET 2 C 2 THR A 99 TRP A 103 -1 N SER A 102 O ALA A 94 SSBOND 1 CYS A 22 CYS A 92 1555 1555 2.02 CRYST1 29.620 41.830 38.520 90.00 95.45 90.00 P 1 21 1 2 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 0.033761 0.000000 0.003221 0.00000 SCALE2 0.000000 0.023906 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026078 0.00000