HEADER IMMUNE SYSTEM 09-APR-02 1LDS TITLE CRYSTAL STRUCTURE OF MONOMERIC HUMAN BETA-2-MICROGLOBULIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 3 CHAIN: A; COMPND 4 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: B2M; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET23A; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PINKWT KEYWDS IMMUNOGLOBULIN CONSTANT DOMAIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR C.H.TRINH,D.P.SMITH,A.P.KALVERDA,S.E.V.PHILLIPS,S.E.RADFORD REVDAT 6 20-NOV-24 1LDS 1 REMARK REVDAT 5 20-SEP-23 1LDS 1 REMARK REVDAT 4 21-DEC-22 1LDS 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1LDS 1 VERSN REVDAT 2 01-APR-03 1LDS 1 JRNL REVDAT 1 31-JUL-02 1LDS 0 JRNL AUTH C.H.TRINH,D.P.SMITH,A.P.KALVERDA,S.E.PHILLIPS,S.E.RADFORD JRNL TITL CRYSTAL STRUCTURE OF MONOMERIC HUMAN BETA-2-MICROGLOBULIN JRNL TITL 2 REVEALS CLUES TO ITS AMYLOIDOGENIC PROPERTIES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 99 9771 2002 JRNL REFN ISSN 0027-8424 JRNL PMID 12119416 JRNL DOI 10.1073/PNAS.152337399 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.70 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) (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 9565 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) : 0.187 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 498 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE : 0.2350 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 51 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 : 809 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 103 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.12500 REMARK 3 B22 (A**2) : -2.09500 REMARK 3 B33 (A**2) : -0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01700 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.23 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) : 0.06 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.448 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.41 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.615 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.827 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.479 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 7.266 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.501 ; 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 AS IMPLEMENTED IN CNS REMARK 4 REMARK 4 1LDS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-02. REMARK 100 THE DEPOSITION ID IS D_1000015863. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9604 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 26.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.07300 REMARK 200 R SYM FOR SHELL (I) : 0.06200 REMARK 200 FOR SHELL : 9.600 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: PDB ENTRY 1DUZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4-8% (W/V) PEG4000, 20% ISOPROPANOL, REMARK 280 100MM SODIUM CITRATE, PH 5.7, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 38.71250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.54550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.71250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.54550 REMARK 290 SMTRY3 4 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 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 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 ARG A 97 REMARK 465 ASP A 98 REMARK 465 MET A 99 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 17 69.07 -150.48 REMARK 500 SER A 57 -85.61 -103.73 REMARK 500 GLU A 74 -5.78 -58.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 100 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 84 O REMARK 620 2 LEU A 87 O 86.1 REMARK 620 3 HOH A 123 O 85.0 170.4 REMARK 620 4 HOH A 138 O 94.7 80.7 96.5 REMARK 620 5 HOH A 141 O 170.8 84.7 104.1 83.4 REMARK 620 6 HOH A 203 O 86.4 83.7 99.2 164.3 93.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DUZ RELATED DB: PDB REMARK 900 HUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) IN COMPLEX REMARK 900 WITH A NONAMERIC PEPTIDE FROM HTLV-1 TAX PROTEIN DBREF 1LDS A 1 99 UNP P61769 B2MG_HUMAN 21 119 SEQADV 1LDS MET A 0 UNP P61769 INITIATING METHIONINE SEQRES 1 A 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 A 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 A 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP SEQRES 4 A 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 A 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 A 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 A 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 A 100 LYS ILE VAL LYS TRP ASP ARG ASP MET HET NA A 100 1 HETNAM NA SODIUM ION FORMUL 2 NA NA 1+ FORMUL 3 HOH *103(H2 O) HELIX 1 1 PRO A 14 GLY A 18 5 5 SHEET 1 A 4 LYS A 6 ARG A 12 0 SHEET 2 A 4 PHE A 22 PHE A 30 -1 O ASN A 24 N TYR A 10 SHEET 3 A 4 PHE A 62 GLU A 69 -1 O LEU A 64 N VAL A 27 SHEET 4 A 4 HIS A 51 PHE A 56 -1 N SER A 55 O TYR A 63 SHEET 1 B 4 GLU A 44 ARG A 45 0 SHEET 2 B 4 GLU A 36 LYS A 41 -1 N LYS A 41 O GLU A 44 SHEET 3 B 4 TYR A 78 ASN A 83 -1 O ALA A 79 N LEU A 40 SHEET 4 B 4 LYS A 91 LYS A 94 -1 O LYS A 91 N VAL A 82 SSBOND 1 CYS A 25 CYS A 80 1555 1555 2.03 LINK O HIS A 84 NA NA A 100 1555 1555 2.35 LINK O LEU A 87 NA NA A 100 1555 1555 2.25 LINK NA NA A 100 O HOH A 123 1555 1555 2.41 LINK NA NA A 100 O HOH A 138 1555 1555 2.39 LINK NA NA A 100 O HOH A 141 1555 1555 2.72 LINK NA NA A 100 O HOH A 203 1555 1555 2.17 CISPEP 1 HIS A 31 PRO A 32 0 0.09 SITE 1 AC1 7 ALA A 15 HIS A 84 LEU A 87 HOH A 123 SITE 2 AC1 7 HOH A 138 HOH A 141 HOH A 203 CRYST1 77.425 29.091 54.644 90.00 121.64 90.00 C 1 2 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 0.012916 0.000000 0.007958 0.00000 SCALE2 0.000000 0.034375 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021495 0.00000