HEADER IMMUNE SYSTEM 08-JUN-19 6K7U TITLE CRYSTAL STRUCTURE OF BETA-2 MICROGLOBULIN (BETA2M) OF BAT (PTEROPUS TITLE 2 ALECTO) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BAT BETA-2-MICROGLOBULIN; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PTEROPUS ALECTO; SOURCE 3 ORGANISM_TAXID: 9402; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: K-12 KEYWDS IMMUNE MOLECULAR, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR D.LU,K.F.LIU,D.ZHANG,C.YUE,Q.LU,H.CHENG,Y.CHAI,J.X.QI,F.G.GAO,W.J.LIU REVDAT 3 04-DEC-19 6K7U 1 TITLE REVDAT 2 25-SEP-19 6K7U 1 TITLE REVDAT 1 18-SEP-19 6K7U 0 JRNL AUTH D.LU,K.LIU,D.ZHANG,C.YUE,Q.LU,H.CHENG,L.WANG,Y.CHAI,J.QI, JRNL AUTH 2 L.F.WANG,G.F.GAO,W.J.LIU JRNL TITL PEPTIDE PRESENTATION BY BAT MHC CLASS I PROVIDES NEW INSIGHT JRNL TITL 2 INTO THE ANTIVIRAL IMMUNITY OF BATS. JRNL REF PLOS BIOL. V. 17 00436 2019 JRNL REFN ESSN 1545-7885 JRNL PMID 31498797 JRNL DOI 10.1371/JOURNAL.PBIO.3000436 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 14900 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 713 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 40.5399 - 2.7367 1.00 3011 141 0.1720 0.1619 REMARK 3 2 2.7367 - 2.1722 1.00 2872 142 0.2122 0.2215 REMARK 3 3 2.1722 - 1.8976 1.00 2861 136 0.1916 0.2132 REMARK 3 4 1.8976 - 1.7241 1.00 2808 146 0.2209 0.2369 REMARK 3 5 1.7241 - 1.6006 0.94 2635 148 0.2528 0.3012 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.160 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 : 0.006 849 REMARK 3 ANGLE : 1.015 1159 REMARK 3 CHIRALITY : 0.086 117 REMARK 3 PLANARITY : 0.007 153 REMARK 3 DIHEDRAL : 26.291 319 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6K7U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1300012457. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97776 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : OSCILLATION CAMERA REMARK 200 DETECTOR MANUFACTURER : SDMS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15045 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.0360 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 8% W/V REMARK 280 POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 28.65350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.65350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 16.85350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.32050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 16.85350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.32050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.65350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 16.85350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.32050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.65350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 16.85350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.32050 REMARK 290 SMTRY3 8 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 176 LIES ON A SPECIAL POSITION. 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 ASN B 98 REMARK 465 THR B 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 SER B 51 172.20 -59.34 REMARK 500 SER B 60 -139.32 50.34 REMARK 500 REMARK 500 REMARK: NULL DBREF 6K7U B 1 99 PDB 6K7U 6K7U 1 99 SEQRES 1 B 99 GLU PRO ARG THR PRO LYS ILE GLN VAL TYR SER ARG HIS SEQRES 2 B 99 PRO ALA GLU ASN GLY LYS PRO ASN TYR LEU ASN CYS TYR SEQRES 3 B 99 VAL TYR GLY PHE HIS PRO PRO GLN ILE GLU ILE ASP LEU SEQRES 4 B 99 LEU LYS ASN GLY GLN LYS MET LYS THR GLU GLN SER ASP SEQRES 5 B 99 LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU LEU VAL SEQRES 6 B 99 HIS THR ASP PHE THR PRO SER THR VAL ASP GLU TYR SER SEQRES 7 B 99 CYS ARG VAL ASN HIS SER SER LEU ALA ALA PRO HIS MET SEQRES 8 B 99 VAL LYS TRP ASP ARG ASN ASN THR FORMUL 2 HOH *87(H2 O) SHEET 1 AA1 4 LYS B 6 SER B 11 0 SHEET 2 AA1 4 ASN B 21 PHE B 30 -1 O TYR B 28 N LYS B 6 SHEET 3 AA1 4 SER B 60 PHE B 69 -1 O THR B 67 N LEU B 23 SHEET 4 AA1 4 GLU B 49 GLN B 50 -1 N GLU B 49 O HIS B 66 SHEET 1 AA2 4 LYS B 6 SER B 11 0 SHEET 2 AA2 4 ASN B 21 PHE B 30 -1 O TYR B 28 N LYS B 6 SHEET 3 AA2 4 SER B 60 PHE B 69 -1 O THR B 67 N LEU B 23 SHEET 4 AA2 4 SER B 54 SER B 56 -1 N SER B 54 O TYR B 62 SHEET 1 AA3 4 GLN B 44 LYS B 45 0 SHEET 2 AA3 4 GLU B 36 LYS B 41 -1 N LYS B 41 O GLN B 44 SHEET 3 AA3 4 TYR B 77 ASN B 82 -1 O ARG B 80 N ASP B 38 SHEET 4 AA3 4 HIS B 90 LYS B 93 -1 O HIS B 90 N VAL B 81 SSBOND 1 CYS B 25 CYS B 79 1555 1555 2.02 CISPEP 1 HIS B 31 PRO B 32 0 2.49 CISPEP 2 HIS B 31 PRO B 32 0 -4.50 CRYST1 33.707 114.641 57.307 90.00 90.00 90.00 C 2 2 21 8 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 0.029667 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008723 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017450 0.00000