HEADER IMMUNE SYSTEM 20-NOV-18 6I8C TITLE CRYSTAL STRUCTURE OF THE MURINE BETA-2-MICROGLOBULIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: B2M; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MHC CLASS I, BETA-2-MICROGLOBULIN, PROTEIN AGGREGATION, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.ACHOUR,T.SANDALOVA,S.RICAGNO,R.SUN REVDAT 6 13-NOV-24 6I8C 1 REMARK REVDAT 5 07-FEB-24 6I8C 1 REMARK REVDAT 4 08-MAR-23 6I8C 1 TITLE REVDAT 3 20-APR-22 6I8C 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQADV SITE ATOM REVDAT 2 12-FEB-20 6I8C 1 JRNL REVDAT 1 02-OCT-19 6I8C 0 JRNL AUTH A.ACHOUR,L.BROGGINI,X.HAN,R.SUN,C.SANTAMBROGIO,J.BURATTO, JRNL AUTH 2 C.VISENTIN,A.BARBIROLI,C.M.G.DE LUCA,P.SORMANNI,F.MODA, JRNL AUTH 3 A.DE SIMONE,T.SANDALOVA,R.GRANDORI,C.CAMILLONI,S.RICAGNO JRNL TITL BIOCHEMICAL AND BIOPHYSICAL COMPARISON OF HUMAN AND MOUSE JRNL TITL 2 BETA-2 MICROGLOBULIN REVEALS THE MOLECULAR DETERMINANTS OF JRNL TITL 3 LOW AMYLOID PROPENSITY. JRNL REF FEBS J. V. 287 546 2020 JRNL REFN ISSN 1742-464X JRNL PMID 31420997 JRNL DOI 10.1111/FEBS.15046 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0230 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 8432 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 + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 450 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 589 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.1760 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 821 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24000 REMARK 3 B22 (A**2) : -1.42000 REMARK 3 B33 (A**2) : 1.66000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.160 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.145 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.017 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 874 ; 0.007 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 782 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1183 ; 1.152 ; 1.685 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1850 ; 0.803 ; 1.650 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 102 ; 7.529 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 43 ;34.651 ;23.488 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 160 ;14.427 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ; 3.970 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 115 ; 0.056 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 936 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 156 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 402 ; 1.544 ; 2.038 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 401 ; 1.542 ; 2.035 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 500 ; 2.454 ; 3.025 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 501 ; 2.452 ; 3.030 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 472 ; 2.038 ; 2.365 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 472 ; 2.038 ; 2.365 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 682 ; 3.256 ; 3.435 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 931 ; 5.511 ;24.336 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 932 ; 5.508 ;24.364 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6I8C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1200012225. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 180 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8882 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.13200 REMARK 200 FOR SHELL : NULL 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: 1BII REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 6000, 100MM TRIS, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 18.12100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.46850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.80150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.46850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.12100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.80150 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 KCAL/MOL 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 TRP A 60 62.90 72.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PGE A 201 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MET A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 201 DBREF 6I8C A 1 101 UNP P01887 B2MG_MOUSE 21 119 SEQADV 6I8C ASP A 85 UNP P01887 ALA 105 ENGINEERED MUTATION SEQRES 1 A 99 ILE GLN LYS THR PRO GLN ILE GLN VAL TYR SER ARG HIS SEQRES 2 A 99 PRO PRO GLU ASN GLY LYS PRO ASN ILE LEU ASN CYS TYR SEQRES 3 A 99 VAL THR GLN PHE HIS PRO PRO HIS ILE GLU ILE GLN MET SEQRES 4 A 99 LEU LYS ASN GLY LYS LYS ILE PRO LYS VAL GLU MET SER SEQRES 5 A 99 ASP MET SER PHE SER LYS ASP TRP SER PHE TYR ILE LEU SEQRES 6 A 99 ALA HIS THR GLU PHE THR PRO THR GLU THR ASP THR TYR SEQRES 7 A 99 ALA CYS ARG VAL LYS HIS ASP SER MET ALA GLU PRO LYS SEQRES 8 A 99 THR VAL TYR TRP ASP ARG ASP MET HET PGE A 201 5 HETNAM PGE TRIETHYLENE GLYCOL FORMUL 2 PGE C6 H14 O4 FORMUL 3 HOH *87(H2 O) SHEET 1 AA1 4 GLN A 6 SER A 11 0 SHEET 2 AA1 4 ASN A 21 PHE A 30 -1 O TYR A 26 N GLN A 8 SHEET 3 AA1 4 SER A 61 PHE A 70 -1 O THR A 68 N LEU A 23 SHEET 4 AA1 4 GLU A 50 MET A 51 -1 N GLU A 50 O HIS A 67 SHEET 1 AA2 4 GLN A 6 SER A 11 0 SHEET 2 AA2 4 ASN A 21 PHE A 30 -1 O TYR A 26 N GLN A 8 SHEET 3 AA2 4 SER A 61 PHE A 70 -1 O THR A 68 N LEU A 23 SHEET 4 AA2 4 SER A 55 SER A 57 -1 N SER A 57 O SER A 61 SHEET 1 AA3 4 LYS A 44 LYS A 45 0 SHEET 2 AA3 4 GLU A 36 LYS A 41 -1 N LYS A 41 O LYS A 44 SHEET 3 AA3 4 TYR A 78 LYS A 83 -1 O ARG A 81 N GLN A 38 SHEET 4 AA3 4 LYS A 91 TYR A 94 -1 O VAL A 93 N CYS A 80 SSBOND 1 CYS A 25 CYS A 80 1555 1555 2.02 CISPEP 1 HIS A 31 PRO A 32 0 10.88 SITE 1 AC1 8 TYR A 10 PHE A 56 LYS A 58 ASP A 96 SITE 2 AC1 8 ARG A 97 ASP A 98 PGE A 201 HOH A 338 SITE 1 AC2 6 ASN A 42 LYS A 58 THR A 75 ASP A 76 SITE 2 AC2 6 ASP A 98 MET A 101 CRYST1 36.242 47.603 64.937 90.00 90.00 90.00 P 21 21 21 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 0.027592 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021007 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015400 0.00000