HEADER IMMUNE SYSTEM 23-JUL-15 5CSB TITLE THE CRYSTAL STRUCTURE OF BETA2-MICROGLOBULIN D76N MUTANT AT ROOM TITLE 2 TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 21-119; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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, CDABP0092, HDCMA22P; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-2 MICROGLOBULIN, AMYLOIDOSIS, ROOM TEMPERATURE, IMMUNOGLOBULIN- KEYWDS 2 LIKE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.DE ROSA,C.S.MOTA,D.DE SANCTIS,M.BOLOGNESI,S.RICAGNO REVDAT 3 10-JAN-24 5CSB 1 REMARK REVDAT 2 27-JUN-18 5CSB 1 JRNL REVDAT 1 10-AUG-16 5CSB 0 JRNL AUTH T.LE MARCHAND,M.DE ROSA,N.SALVI,B.M.SALA,L.B.ANDREAS, JRNL AUTH 2 E.BARBET-MASSIN,P.SORMANNI,A.BARBIROLI,R.PORCARI, JRNL AUTH 3 C.SOUSA MOTA,D.DE SANCTIS,M.BOLOGNESI,L.EMSLEY,V.BELLOTTI, JRNL AUTH 4 M.BLACKLEDGE,C.CAMILLONI,G.PINTACUDA,S.RICAGNO JRNL TITL CONFORMATIONAL DYNAMICS IN CRYSTALS REVEAL THE MOLECULAR JRNL TITL 2 BASES FOR D76N BETA-2 MICROGLOBULIN AGGREGATION PROPENSITY. JRNL REF NAT COMMUN V. 9 1658 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29695721 JRNL DOI 10.1038/S41467-018-04078-Y REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 10182 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1017 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 45.0450 - 3.2880 0.92 1359 152 0.1643 0.1917 REMARK 3 2 3.2880 - 2.6099 0.92 1327 147 0.1886 0.2296 REMARK 3 3 2.6099 - 2.2800 0.90 1281 142 0.1799 0.2499 REMARK 3 4 2.2800 - 2.0715 0.92 1309 146 0.1930 0.2409 REMARK 3 5 2.0715 - 1.9230 0.91 1310 146 0.1857 0.2607 REMARK 3 6 1.9230 - 1.8097 0.90 1270 139 0.2121 0.2473 REMARK 3 7 1.8097 - 1.7190 0.92 1309 145 0.2512 0.2777 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.230 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 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 : 0.009 937 REMARK 3 ANGLE : 1.293 1283 REMARK 3 CHIRALITY : 0.050 136 REMARK 3 PLANARITY : 0.005 168 REMARK 3 DIHEDRAL : 13.365 371 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.2456 4.7056 -17.2191 REMARK 3 T TENSOR REMARK 3 T11: 0.1469 T22: 0.1549 REMARK 3 T33: 0.2308 T12: -0.0322 REMARK 3 T13: 0.0306 T23: 0.0118 REMARK 3 L TENSOR REMARK 3 L11: 7.5100 L22: 4.3783 REMARK 3 L33: 4.1028 L12: -0.1848 REMARK 3 L13: -5.5585 L23: 0.4284 REMARK 3 S TENSOR REMARK 3 S11: -0.0205 S12: -0.1759 S13: 0.3989 REMARK 3 S21: -0.2463 S22: 0.3103 S23: -0.4824 REMARK 3 S31: -0.1879 S32: 0.8025 S33: -0.1849 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 6 THROUGH 41 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.0752 14.9709 1.0645 REMARK 3 T TENSOR REMARK 3 T11: 0.1179 T22: 0.1324 REMARK 3 T33: 0.2069 T12: 0.0067 REMARK 3 T13: -0.0078 T23: -0.0351 REMARK 3 L TENSOR REMARK 3 L11: 2.6430 L22: 1.1621 REMARK 3 L33: 6.1400 L12: -0.2964 REMARK 3 L13: 0.7878 L23: 0.5026 REMARK 3 S TENSOR REMARK 3 S11: -0.0356 S12: -0.3001 S13: 0.3198 REMARK 3 S21: 0.1133 S22: 0.1141 S23: -0.0442 REMARK 3 S31: -0.1830 S32: -0.1452 S33: -0.0123 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 42 THROUGH 61 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.9214 17.8412 -5.1534 REMARK 3 T TENSOR REMARK 3 T11: 0.2684 T22: 0.3329 REMARK 3 T33: 0.3079 T12: 0.0246 REMARK 3 T13: -0.0608 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 4.5367 L22: 4.3503 REMARK 3 L33: 4.7790 L12: 0.7955 REMARK 3 L13: -4.5629 L23: -1.1903 REMARK 3 S TENSOR REMARK 3 S11: 0.5164 S12: 0.5272 S13: 0.5239 REMARK 3 S21: 0.1674 S22: -0.2057 S23: 0.2789 REMARK 3 S31: -0.6339 S32: -0.7327 S33: -0.2701 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 62 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.9444 11.3418 1.5378 REMARK 3 T TENSOR REMARK 3 T11: 0.1355 T22: 0.2003 REMARK 3 T33: 0.2179 T12: -0.0027 REMARK 3 T13: 0.0124 T23: 0.0099 REMARK 3 L TENSOR REMARK 3 L11: 3.2820 L22: 2.4165 REMARK 3 L33: 8.1750 L12: 0.0101 REMARK 3 L13: -0.7387 L23: 2.1782 REMARK 3 S TENSOR REMARK 3 S11: 0.0360 S12: -0.5542 S13: 0.0559 REMARK 3 S21: 0.3405 S22: -0.1635 S23: 0.1775 REMARK 3 S31: 0.4046 S32: -0.4963 S33: 0.1153 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5CSB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000212111. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10186 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.719 REMARK 200 RESOLUTION RANGE LOW (A) : 45.045 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4FXL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.1M SODIUM ACETATE, 15% REMARK 280 GLYCEROL, 0.2M AMMONIUM ACETATE, PH 4.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 23.25543 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.66000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.48350 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 23.25543 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.66000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 31.48350 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 75 OD2 ASP A 98 4455 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 17 -53.75 -127.83 REMARK 500 ASN A 42 16.29 58.02 REMARK 500 SER A 57 -87.32 -98.99 REMARK 500 LYS A 58 -168.87 -77.68 REMARK 500 TRP A 60 -65.97 -97.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FXL RELATED DB: PDB REMARK 900 SAME STRUCTURE AT 100 K DBREF 5CSB A 1 99 UNP P61769 B2MG_HUMAN 21 119 SEQADV 5CSB MET A 0 UNP P61769 INITIATING METHIONINE SEQADV 5CSB ASN A 76 UNP P61769 ASP 96 ENGINEERED MUTATION 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 ASN 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 FORMUL 2 HOH *37(H2 O) SHEET 1 AA1 4 LYS A 6 ARG A 12 0 SHEET 2 AA1 4 PHE A 22 PHE A 30 -1 O TYR A 26 N GLN A 8 SHEET 3 AA1 4 PHE A 62 GLU A 69 -1 O TYR A 66 N CYS A 25 SHEET 4 AA1 4 HIS A 51 PHE A 56 -1 N ASP A 53 O LEU A 65 SHEET 1 AA2 4 GLU A 44 ARG A 45 0 SHEET 2 AA2 4 GLU A 36 LYS A 41 -1 N LYS A 41 O GLU A 44 SHEET 3 AA2 4 TYR A 78 ASN A 83 -1 O ALA A 79 N LEU A 40 SHEET 4 AA2 4 LYS A 91 LYS A 94 -1 O VAL A 93 N CYS A 80 SSBOND 1 CYS A 25 CYS A 80 1555 1555 2.04 CISPEP 1 HIS A 31 PRO A 32 0 -0.51 CRYST1 56.000 29.320 63.678 90.00 98.57 90.00 I 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 0.017857 0.000000 0.002692 0.00000 SCALE2 0.000000 0.034107 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015881 0.00000