HEADER SIGNALING PROTEIN 26-MAR-07 2P9R TITLE HUMAN ALPHA2-MACROGLOGULIN IS COMPOSED OF MULTIPLE DOMAINS, AS TITLE 2 PREDICTED BY HOMOLOGY WITH COMPLEMENT COMPONENT C3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-2-MACROGLOBULIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALPHA-2-M; 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: A2M; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SG13009; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS HUMAN ALPHA2-MACROGLOBULIN, MG2 DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.DOAN REVDAT 4 21-FEB-24 2P9R 1 REMARK REVDAT 3 24-FEB-09 2P9R 1 VERSN REVDAT 2 30-OCT-07 2P9R 1 JRNL REVDAT 1 21-AUG-07 2P9R 0 JRNL AUTH N.DOAN,P.G.GETTINS JRNL TITL HUMAN ALPHA2-MACROGLOBULIN IS COMPOSED OF MULTIPLE DOMAINS, JRNL TITL 2 AS PREDICTED BY HOMOLOGY WITH COMPLEMENT COMPONENT C3. JRNL REF BIOCHEM.J. V. 407 23 2007 JRNL REFN ISSN 0264-6021 JRNL PMID 17608619 JRNL DOI 10.1042/BJ20070764 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 13500 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 1611 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 65 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) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 2P9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000042144. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13500 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 48.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 23.00 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) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 11% PEG 3350, 200MM DI-AMMONIUM REMARK 280 HYDROGEN CITRATE, PH 6.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.03500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.40500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.40500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 90.05250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.40500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.40500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.01750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.40500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.40500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 90.05250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.40500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.40500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.01750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 60.03500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: BIOLOGICAL ASSEMBLY IS A MONOMER. 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLU B 200 REMARK 465 PHE B 201 REMARK 465 VAL B 202 REMARK 465 LEU B 203 REMARK 465 PRO B 204 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 O ASP B 129 N ASN B 131 2.14 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 ASN A 131 8.41 83.80 REMARK 500 SER A 157 63.09 34.50 REMARK 500 GLU A 200 -31.73 -149.80 REMARK 500 PHE A 201 131.99 75.52 REMARK 500 ASP B 129 178.18 -59.72 REMARK 500 GLU B 130 76.77 -45.84 REMARK 500 ASN B 131 149.04 65.70 REMARK 500 PHE B 132 -142.53 80.02 REMARK 500 HIS B 133 146.33 -14.89 REMARK 500 ASN B 136 66.29 -100.09 REMARK 500 SER B 157 73.19 27.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 2P9R A 103 204 UNP P01023 A2MG_HUMAN 126 227 DBREF 2P9R B 103 204 UNP P01023 A2MG_HUMAN 126 227 SEQRES 1 A 102 ASP SER LEU VAL PHE VAL GLN THR ASP LYS SER ILE TYR SEQRES 2 A 102 LYS PRO GLY GLN THR VAL LYS PHE ARG VAL VAL SER MET SEQRES 3 A 102 ASP GLU ASN PHE HIS PRO LEU ASN GLU LEU ILE PRO LEU SEQRES 4 A 102 VAL TYR ILE GLN ASP PRO LYS GLY ASN ARG ILE ALA GLN SEQRES 5 A 102 TRP GLN SER PHE GLN LEU GLU GLY GLY LEU LYS GLN PHE SEQRES 6 A 102 SER PHE PRO LEU SER SER GLU PRO PHE GLN GLY SER TYR SEQRES 7 A 102 LYS VAL VAL VAL GLN LYS LYS SER GLY GLY ARG THR GLU SEQRES 8 A 102 HIS PRO PHE THR VAL GLU GLU PHE VAL LEU PRO SEQRES 1 B 102 ASP SER LEU VAL PHE VAL GLN THR ASP LYS SER ILE TYR SEQRES 2 B 102 LYS PRO GLY GLN THR VAL LYS PHE ARG VAL VAL SER MET SEQRES 3 B 102 ASP GLU ASN PHE HIS PRO LEU ASN GLU LEU ILE PRO LEU SEQRES 4 B 102 VAL TYR ILE GLN ASP PRO LYS GLY ASN ARG ILE ALA GLN SEQRES 5 B 102 TRP GLN SER PHE GLN LEU GLU GLY GLY LEU LYS GLN PHE SEQRES 6 B 102 SER PHE PRO LEU SER SER GLU PRO PHE GLN GLY SER TYR SEQRES 7 B 102 LYS VAL VAL VAL GLN LYS LYS SER GLY GLY ARG THR GLU SEQRES 8 B 102 HIS PRO PHE THR VAL GLU GLU PHE VAL LEU PRO FORMUL 3 HOH *65(H2 O) HELIX 1 1 ASP A 129 HIS A 133 5 5 SHEET 1 A 3 LEU A 105 THR A 110 0 SHEET 2 A 3 THR A 120 MET A 128 -1 O MET A 128 N LEU A 105 SHEET 3 A 3 LEU A 164 PRO A 170 -1 O PHE A 167 N PHE A 123 SHEET 1 B10 ILE A 114 TYR A 115 0 SHEET 2 B10 ARG A 191 VAL A 198 1 O THR A 197 N TYR A 115 SHEET 3 B10 GLY A 178 GLN A 185 -1 N TYR A 180 O PHE A 196 SHEET 4 B10 LEU A 138 GLN A 145 -1 N TYR A 143 O VAL A 183 SHEET 5 B10 ARG A 151 GLN A 159 -1 O TRP A 155 N VAL A 142 SHEET 6 B10 ARG B 151 GLN B 159 -1 O GLN B 154 N GLN A 154 SHEET 7 B10 LEU B 138 GLN B 145 -1 N VAL B 142 O TRP B 155 SHEET 8 B10 GLY B 178 GLN B 185 -1 O VAL B 183 N TYR B 143 SHEET 9 B10 ARG B 191 VAL B 198 -1 O PHE B 196 N TYR B 180 SHEET 10 B10 ILE B 114 TYR B 115 1 N TYR B 115 O THR B 197 SHEET 1 C 3 LEU B 105 THR B 110 0 SHEET 2 C 3 THR B 120 MET B 128 -1 O VAL B 126 N PHE B 107 SHEET 3 C 3 LEU B 164 PRO B 170 -1 O PHE B 169 N VAL B 121 CRYST1 68.810 68.810 120.070 90.00 90.00 90.00 P 43 21 2 16 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 0.014533 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014533 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008328 0.00000