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