HEADER PROTEIN BINDING 28-JAN-00 1EDY TITLE CRYSTAL STRUCTURE OF RAT ALPHA 1-MACROGLOBULIN RECEPTOR BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA 1-MACROGLOBULIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 TISSUE: PLASMA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS BETA SANDWICH, PSEUDO-SYMMETRIC DIMER, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR T.XIAO,D.L.DECAMP,S.R.SPRANG REVDAT 4 07-FEB-24 1EDY 1 REMARK REVDAT 3 24-FEB-09 1EDY 1 VERSN REVDAT 2 01-APR-03 1EDY 1 JRNL REVDAT 1 01-DEC-00 1EDY 0 JRNL AUTH T.XIAO,D.L.DECAMP,S.R.SPRAN JRNL TITL STRUCTURE OF A RAT ALPHA 1-MACROGLOBULIN RECEPTOR-BINDING JRNL TITL 2 DOMAIN DIMER. JRNL REF PROTEIN SCI. V. 9 1889 2000 JRNL REFN ISSN 0961-8368 JRNL PMID 11106161 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.88 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) (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 14147 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1434 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 : 2142 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 13.98900 REMARK 3 B22 (A**2) : 7.88400 REMARK 3 B33 (A**2) : -21.87300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 9.09700 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.32 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) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.42 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.278 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: MAXIMUM LIKELIHOOD TARGET USING REMARK 3 AMPLITUDES REMARK 4 REMARK 4 1EDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1000010477. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14814 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 3.280 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.28 REMARK 200 R MERGE FOR SHELL (I) : 0.19000 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 (%): 56.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG6000, CALCIUM CHLORIDE, HEPES, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 18.07550 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 128.75400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 18.07550 REMARK 350 BIOMT3 2 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 SER B 133 REMARK 465 SER B 134 REMARK 465 ASP B 135 REMARK 465 SER B 136 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 16 25.38 -152.67 REMARK 500 PHE A 17 -1.59 -57.03 REMARK 500 GLU A 21 -74.64 -86.71 REMARK 500 PRO A 131 56.55 -68.56 REMARK 500 ASN B 42 -159.75 -95.33 REMARK 500 ASN B 76 -164.89 -101.90 REMARK 500 THR B 88 -163.71 -120.97 REMARK 500 PRO B 131 12.54 -58.95 REMARK 500 REMARK 500 REMARK: NULL DBREF 1EDY A 3 136 UNP Q63332 Q63332_RAT 1362 1495 DBREF 1EDY B 3 136 UNP Q63332 Q63332_RAT 1362 1495 SEQRES 1 A 134 GLU ALA PRO PHE THR LEU LYS VAL ASN THR LEU PRO LEU SEQRES 2 A 134 ASN PHE ASP LYS ALA GLU HIS HIS ARG LYS PHE GLN ILE SEQRES 3 A 134 HIS ILE ASN VAL SER TYR ILE GLY GLU ARG PRO ASN SER SEQRES 4 A 134 ASN MET VAL ILE VAL ASP VAL LYS MET VAL SER GLY PHE SEQRES 5 A 134 ILE PRO VAL LYS PRO SER VAL LYS LYS LEU GLN ASP GLN SEQRES 6 A 134 SER ASN ILE GLN ARG THR GLU VAL ASN THR ASN HIS VAL SEQRES 7 A 134 LEU ILE TYR ILE GLU LYS LEU THR ASN GLN THR MET GLY SEQRES 8 A 134 PHE SER PHE ALA VAL GLU GLN ASP ILE PRO VAL LYS ASN SEQRES 9 A 134 LEU LYS PRO ALA PRO VAL LYS VAL TYR ASP TYR TYR GLU SEQRES 10 A 134 THR ASP GLU PHE ALA ILE GLU GLU TYR SER ALA PRO PHE SEQRES 11 A 134 SER SER ASP SER SEQRES 1 B 134 GLU ALA PRO PHE THR LEU LYS VAL ASN THR LEU PRO LEU SEQRES 2 B 134 ASN PHE ASP LYS ALA GLU HIS HIS ARG LYS PHE GLN ILE SEQRES 3 B 134 HIS ILE ASN VAL SER TYR ILE GLY GLU ARG PRO ASN SER SEQRES 4 B 134 ASN MET VAL ILE VAL ASP VAL LYS MET VAL SER GLY PHE SEQRES 5 B 134 ILE PRO VAL LYS PRO SER VAL LYS LYS LEU GLN ASP GLN SEQRES 6 B 134 SER ASN ILE GLN ARG THR GLU VAL ASN THR ASN HIS VAL SEQRES 7 B 134 LEU ILE TYR ILE GLU LYS LEU THR ASN GLN THR MET GLY SEQRES 8 B 134 PHE SER PHE ALA VAL GLU GLN ASP ILE PRO VAL LYS ASN SEQRES 9 B 134 LEU LYS PRO ALA PRO VAL LYS VAL TYR ASP TYR TYR GLU SEQRES 10 B 134 THR ASP GLU PHE ALA ILE GLU GLU TYR SER ALA PRO PHE SEQRES 11 B 134 SER SER ASP SER FORMUL 3 HOH *94(H2 O) HELIX 1 1 VAL A 57 LYS A 63 1 7 HELIX 2 2 LEU A 64 GLN A 67 5 4 HELIX 3 3 VAL B 57 LYS B 63 1 7 HELIX 4 4 LEU B 64 GLN B 67 5 4 SHEET 1 A 4 PHE A 6 PRO A 14 0 SHEET 2 A 4 LYS A 25 TYR A 34 -1 N GLN A 27 O LEU A 13 SHEET 3 A 4 MET A 92 GLN A 100 -1 O MET A 92 N VAL A 32 SHEET 4 A 4 PHE A 54 PRO A 56 -1 O ILE A 55 N GLU A 99 SHEET 1 B 5 ILE A 70 ASN A 76 0 SHEET 2 B 5 HIS A 79 ILE A 84 -1 O HIS A 79 N ASN A 76 SHEET 3 B 5 VAL A 44 LYS A 49 -1 N VAL A 44 O ILE A 84 SHEET 4 B 5 ALA A 110 ASP A 116 -1 O PRO A 111 N LYS A 49 SHEET 5 B 5 PHE A 123 TYR A 128 -1 O ALA A 124 N VAL A 114 SHEET 1 C 4 PHE B 6 LEU B 15 0 SHEET 2 C 4 LYS B 25 TYR B 34 -1 O LYS B 25 N LEU B 15 SHEET 3 C 4 MET B 92 GLN B 100 -1 O MET B 92 N VAL B 32 SHEET 4 C 4 PHE B 54 PRO B 56 -1 O ILE B 55 N GLU B 99 SHEET 1 D 5 ILE B 70 ASN B 76 0 SHEET 2 D 5 HIS B 79 ILE B 84 -1 O HIS B 79 N ASN B 76 SHEET 3 D 5 VAL B 44 LYS B 49 -1 O VAL B 44 N ILE B 84 SHEET 4 D 5 ALA B 110 ASP B 116 -1 O PRO B 111 N LYS B 49 SHEET 5 D 5 PHE B 123 TYR B 128 -1 O ALA B 124 N VAL B 114 CRYST1 64.377 36.151 77.978 90.00 105.88 90.00 P 1 21 1 4 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 0.015533 0.000000 0.004418 0.00000 SCALE2 0.000000 0.027662 -0.000001 0.00000 SCALE3 0.000000 0.000000 0.013333 0.00000