HEADER IMMUNE SYSTEM 04-JAN-00 1DQL TITLE CRYSTAL STRUCTURE OF AN UNLIGANDED (NATIVE) FV FROM A HUMAN IGM ANTI- TITLE 2 PEPTIDE ANTIBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: IGM MEZ IMMUNOGLOBULIN; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: LIGHT CHAIN VARIABLE DOMAIN FRAGMENT; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: IGM MEZ IMMUNOGLOBULIN; COMPND 7 CHAIN: H; COMPND 8 FRAGMENT: HEAVY CHAIN VARIABLE DOMAIN FRAGMENT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606 KEYWDS IMMUNOGLOBULIN FOLD, ANTIBODY, IGM, FV, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR P.A.RAMSLAND,L.SHAN,C.R.MOOMAW,C.A.SLAUGHTER,L.W.GUDDAT,A.B.EDMUNDSON REVDAT 4 25-DEC-19 1DQL 1 SEQRES LINK REVDAT 3 04-OCT-17 1DQL 1 REMARK REVDAT 2 24-FEB-09 1DQL 1 VERSN REVDAT 1 04-OCT-00 1DQL 0 JRNL AUTH P.A.RAMSLAND,L.SHAN,C.R.MOOMAW,C.A.SLAUGHTER,Z.FAN, JRNL AUTH 2 L.W.GUDDAT,A.B.EDMUNDSON JRNL TITL AN UNUSUAL HUMAN IGM ANTIBODY WITH A PROTRUDING HCDR3 AND JRNL TITL 2 HIGH AVIDITY FOR ITS PEPTIDE LIGANDS. JRNL REF MOL.IMMUNOL. V. 37 295 2000 JRNL REFN ISSN 0161-5890 JRNL PMID 11000403 JRNL DOI 10.1016/S0161-5890(00)00049-3 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 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) (%) : 83.4 REMARK 3 NUMBER OF REFLECTIONS : 6963 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) : 0.181 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.000 REMARK 3 FREE R VALUE TEST SET COUNT : 764 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 40.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 502 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE : 0.3790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 65 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.047 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1740 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.90 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) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.38 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.57 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.350 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.25 REMARK 3 BSOL : 14.31 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PCA.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : PCA.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DQL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1000010298. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-90 REMARK 200 TEMPERATURE (KELVIN) : 288 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7111 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.580 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.4 REMARK 200 DATA REDUNDANCY : 2.250 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 40.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.20 REMARK 200 R MERGE FOR SHELL (I) : 0.16700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6-8% (W/V) PEG 8000, 0.05% (W/V) REMARK 280 SODIUM AZIDE, PH 7.0, MICROSEEDING, SITTING DROP, TEMPERATURE REMARK 280 295K 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 30.56500 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 300 REMARK: THE MEZ FV IS A NON-COVALENT HETERODIMER OF VL (CHAIN L) REMARK 300 AND VH (CHAIN H) 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H 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: 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 L 30 -118.29 55.79 REMARK 500 ALA L 51 -43.90 64.30 REMARK 500 ALA L 84 -176.20 -179.21 REMARK 500 SER L 93 -149.03 -137.25 REMARK 500 ASP H 74 14.35 -68.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 1DQL L 1 106 PDB 1DQL 1DQL 1 106 DBREF 1DQL H 1 123 PDB 1DQL 1DQL 1 123 SEQRES 1 L 106 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 106 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 106 GLN ASP ILE ARG ASN ASP LEU GLY TRP TYR GLN GLN LYS SEQRES 4 L 106 PRO GLY LYS ALA PRO LYS LYS LEU ILE TYR ALA ALA SER SEQRES 5 L 106 SER LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 106 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 106 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS LEU GLN GLN SEQRES 8 L 106 ASN SER ASN TRP THR PHE GLY GLN GLY THR LYS VAL ASP SEQRES 9 L 106 ILE LYS SEQRES 1 H 123 PCA VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 123 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 123 PHE THR PHE SER SER TYR ALA MET HIS TRP VAL ARG GLN SEQRES 4 H 123 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA VAL ILE SER SEQRES 5 H 123 SER ASP GLY GLY ASN LYS TYR TYR THR ASP SER VAL LYS SEQRES 6 H 123 GLY ARG PHE THR ILE SER ARG ASN ASP SER LYS ASN THR SEQRES 7 H 123 LEU TYR LEU GLN MET ASN SER LEU ARG THR GLU ASP THR SEQRES 8 H 123 ALA VAL PHE TYR CYS ALA ARG GLY ASN PRO PRO TYR SER SEQRES 9 H 123 SER GLY TRP GLY GLY GLY ASP TYR TRP GLY GLN GLY THR SEQRES 10 H 123 MET VAL THR VAL SER SER MODRES 1DQL PCA H 1 GLN PYROGLUTAMIC ACID HET PCA H 1 8 HETNAM PCA PYROGLUTAMIC ACID FORMUL 2 PCA C5 H7 N O3 FORMUL 3 HOH *18(H2 O) HELIX 1 1 THR H 28 TYR H 32 5 5 HELIX 2 2 ASP H 62 VAL H 64 5 3 HELIX 3 3 ARG H 87 THR H 91 5 5 SHEET 1 A 4 THR L 5 SER L 7 0 SHEET 2 A 4 VAL L 19 ARG L 24 -1 O THR L 22 N SER L 7 SHEET 3 A 4 ASP L 70 ILE L 75 -1 N PHE L 71 O CYS L 23 SHEET 4 A 4 PHE L 62 SER L 67 -1 O SER L 63 N THR L 74 SHEET 1 B 5 SER L 53 LEU L 54 0 SHEET 2 B 5 LYS L 45 TYR L 49 -1 N TYR L 49 O SER L 53 SHEET 3 B 5 LEU L 33 GLN L 38 -1 O TRP L 35 N LEU L 47 SHEET 4 B 5 THR L 85 GLN L 90 -1 O THR L 85 N GLN L 38 SHEET 5 B 5 THR L 96 PHE L 97 -1 O THR L 96 N GLN L 90 SHEET 1 C 6 SER L 53 LEU L 54 0 SHEET 2 C 6 LYS L 45 TYR L 49 -1 N TYR L 49 O SER L 53 SHEET 3 C 6 LEU L 33 GLN L 38 -1 O TRP L 35 N LEU L 47 SHEET 4 C 6 THR L 85 GLN L 90 -1 O THR L 85 N GLN L 38 SHEET 5 C 6 THR L 101 ILE L 105 -1 O THR L 101 N TYR L 86 SHEET 6 C 6 SER L 10 ALA L 13 1 O LEU L 11 N ASP L 104 SHEET 1 D 4 GLN H 3 SER H 7 0 SHEET 2 D 4 LEU H 18 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 D 4 THR H 78 MET H 83 -1 O LEU H 79 N CYS H 22 SHEET 4 D 4 PHE H 68 ASN H 73 -1 O THR H 69 N GLN H 82 SHEET 1 E 6 LEU H 11 VAL H 12 0 SHEET 2 E 6 THR H 117 VAL H 121 1 O THR H 120 N VAL H 12 SHEET 3 E 6 ALA H 92 ARG H 98 -1 O ALA H 92 N VAL H 119 SHEET 4 E 6 MET H 34 GLN H 39 -1 N HIS H 35 O ALA H 97 SHEET 5 E 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 E 6 LYS H 58 TYR H 60 -1 N TYR H 59 O VAL H 50 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.03 SSBOND 2 CYS H 22 CYS H 96 1555 1555 2.03 LINK C PCA H 1 N VAL H 2 1555 1555 1.32 CISPEP 1 SER L 7 PRO L 8 0 0.88 CRYST1 53.570 61.130 42.200 90.00 96.90 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 0.018667 0.000000 0.002259 0.00000 SCALE2 0.000000 0.016359 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023870 0.00000 MASTER 236 0 1 3 25 0 0 6 0 0 0 19 END