HEADER IMMUNE SYSTEM 22-JUN-08 3DJ9 TITLE CRYSTAL STRUCTURE OF AN ISOLATED, UNGLYCOSYLATED ANTIBODY CH2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: IG GAMMA-1 CHAIN C REGION; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CH2 CONSTANT DOMAIN; 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: IGHG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TG1; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCOMB3X KEYWDS ANTIBODY, IMMUNOGLOBULIN, CH2 DOMAIN, GLYCOPROTEIN, IMMUNOGLOBULIN C KEYWDS 2 REGION, IMMUNOGLOBULIN DOMAIN, SECRETED, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR P.PRABAKARAN,B.K.VU,J.GAN,D.S.DIMITROV,X.JI REVDAT 6 01-NOV-23 3DJ9 1 REMARK REVDAT 5 30-AUG-23 3DJ9 1 AUTHOR JRNL REVDAT 4 21-DEC-16 3DJ9 1 TITLE REVDAT 3 05-SEP-12 3DJ9 1 JRNL VERSN REVDAT 2 24-FEB-09 3DJ9 1 VERSN REVDAT 1 16-SEP-08 3DJ9 0 JRNL AUTH P.PRABAKARAN,B.K.VU,J.GAN,Y.FENG,D.S.DIMITROV,X.JI JRNL TITL STRUCTURE OF AN ISOLATED UNGLYCOSYLATED ANTIBODY C(H)2 JRNL TITL 2 DOMAIN. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 64 1062 2008 JRNL REFN ISSN 0907-4449 JRNL PMID 18931413 JRNL DOI 10.1107/S0907444908025274 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX PHENIX.REFINE REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.170 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 10493 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 542 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 26.3640 - 3.6380 1.00 1203 64 0.1660 0.1610 REMARK 3 2 3.6380 - 2.8890 1.00 1166 72 0.1890 0.2200 REMARK 3 3 2.8890 - 2.5240 0.99 1171 55 0.2370 0.2700 REMARK 3 4 2.5240 - 2.2930 0.99 1151 75 0.2300 0.2700 REMARK 3 5 2.2930 - 2.1290 0.98 1138 58 0.2050 0.2440 REMARK 3 6 2.1290 - 2.0030 0.98 1135 60 0.2080 0.2890 REMARK 3 7 2.0030 - 1.9030 0.97 1133 61 0.2070 0.2060 REMARK 3 8 1.9030 - 1.8200 0.87 1007 52 0.2270 0.2280 REMARK 3 9 1.8200 - 1.7500 0.72 847 45 0.2360 0.3110 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 53.72 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.40900 REMARK 3 B22 (A**2) : -3.70700 REMARK 3 B33 (A**2) : 8.11600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.15600 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 883 REMARK 3 ANGLE : 1.460 1191 REMARK 3 CHIRALITY : 0.090 137 REMARK 3 PLANARITY : 0.008 148 REMARK 3 DIHEDRAL : 19.712 325 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE REFINEMENT WAS DONE MAINLY WITH CNS REMARK 3 1.1 AND FINISHED WITH PHENIX REMARK 4 REMARK 4 3DJ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000048106. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PROTEUM 300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11044 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 91.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 57.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.11600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.400 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: 1HZH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 1500, PH 7.2, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 292K 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 20.33900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 LYS A 340 -57.60 -147.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HZH RELATED DB: PDB REMARK 900 THE CH2 CONSTANT DOMAIN OF THE INTACT HUMAN IGG B12, CHAIN H AND REMARK 900 RESIDUES 246-352 REMARK 900 RELATED ID: 1OQO RELATED DB: PDB REMARK 900 THE CH2 CONSTANT DOMAIN OF THE FC, CHAIN A,B AND RESIDUES 1-107 REMARK 900 RELATED ID: 2DTQ RELATED DB: PDB REMARK 900 THE CH2 CONSTANT DOMAIN OF THE FC FRAGMENT FROM HUMAN REMARK 900 IMMUNOGLOBULIN G1, CHAIN A,B AND RESIDUES 12-118 REMARK 900 RELATED ID: 2DTS RELATED DB: PDB REMARK 900 THE CH2 CONSTANT DOMAIN OF THE FC FRAGMENT FROM HUMAN REMARK 900 IMMUNOGLOBULIN G1, CHAIN A,B AND RESIDUES 12-118 DBREF 3DJ9 A 236 342 UNP P01857 IGHG1_HUMAN 119 225 SEQRES 1 A 107 GLY GLY PRO SER VAL PHE LEU PHE PRO PRO LYS PRO LYS SEQRES 2 A 107 ASP THR LEU MET ILE SER ARG THR PRO GLU VAL THR CYS SEQRES 3 A 107 VAL VAL VAL ASP VAL SER HIS GLU ASP PRO GLU VAL LYS SEQRES 4 A 107 PHE ASN TRP TYR VAL ASP GLY VAL GLU VAL HIS ASN ALA SEQRES 5 A 107 LYS THR LYS PRO ARG GLU GLU GLN TYR ASN SER THR TYR SEQRES 6 A 107 ARG VAL VAL SER VAL LEU THR VAL LEU HIS GLN ASP TRP SEQRES 7 A 107 LEU ASN GLY LYS GLU TYR LYS CYS LYS VAL SER ASN LYS SEQRES 8 A 107 ALA LEU PRO ALA PRO ILE GLU LYS THR ILE SER LYS ALA SEQRES 9 A 107 LYS GLY GLN FORMUL 2 HOH *111(H2 O) HELIX 1 1 LYS A 246 MET A 252 1 7 HELIX 2 2 LEU A 309 ASN A 315 1 7 SHEET 1 A 4 SER A 239 PHE A 243 0 SHEET 2 A 4 GLU A 258 VAL A 266 -1 O VAL A 262 N PHE A 241 SHEET 3 A 4 TYR A 300 THR A 307 -1 O TYR A 300 N VAL A 266 SHEET 4 A 4 LYS A 288 THR A 289 -1 N LYS A 288 O VAL A 305 SHEET 1 B 4 SER A 239 PHE A 243 0 SHEET 2 B 4 GLU A 258 VAL A 266 -1 O VAL A 262 N PHE A 241 SHEET 3 B 4 TYR A 300 THR A 307 -1 O TYR A 300 N VAL A 266 SHEET 4 B 4 GLU A 293 GLU A 294 -1 N GLU A 293 O ARG A 301 SHEET 1 C 4 VAL A 282 VAL A 284 0 SHEET 2 C 4 LYS A 274 VAL A 279 -1 N VAL A 279 O VAL A 282 SHEET 3 C 4 TYR A 319 SER A 324 -1 O LYS A 322 N ASN A 276 SHEET 4 C 4 ILE A 332 ILE A 336 -1 O ILE A 332 N VAL A 323 SSBOND 1 CYS A 261 CYS A 321 1555 1555 2.04 CRYST1 36.144 40.678 39.131 90.00 106.74 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 0.027667 0.000000 0.008320 0.00000 SCALE2 0.000000 0.024583 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026686 0.00000