HEADER IMMUNE SYSTEM 26-APR-07 2YXF
TITLE THE HIGH RESOLUTION CRYSTAL STRUCTURE OF BETA2-MICROGLOBULIN UNDER
TITLE 2 PHYSIOLOGICAL CONDITIONS
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;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) PLYSS;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHIKARU1A
KEYWDS IMMUNE SYSTEM
EXPDTA X-RAY DIFFRACTION
AUTHOR K.IWATA,T.MATSUURA,A.NAKAGAWA,Y.GOTO
REVDAT 3 25-OCT-23 2YXF 1 SEQADV
REVDAT 2 24-FEB-09 2YXF 1 VERSN
REVDAT 1 30-OCT-07 2YXF 0
JRNL AUTH K.IWATA,T.MATSUURA,K.SAKURAI,A.NAKAGAWA,Y.GOTO
JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURE OF {BETA}2-MICROGLOBULIN
JRNL TITL 2 FORMED AT PH 7.0
JRNL REF J.BIOCHEM.(TOKYO) V. 142 413 2007
JRNL REFN ISSN 0021-924X
JRNL PMID 17646174
JRNL DOI 10.1093/JB/MVM148
REMARK 2
REMARK 2 RESOLUTION. 1.13 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.13
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.49
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 36904
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) : 0.184
REMARK 3 R VALUE (WORKING SET) : 0.184
REMARK 3 FREE R VALUE : 0.195
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1948
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) : 1.13
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.16
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2701
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.1880
REMARK 3 BIN FREE R VALUE SET COUNT : 152
REMARK 3 BIN FREE R VALUE : 0.2210
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 828
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 91
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 9.46
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.11
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.38000
REMARK 3 B22 (A**2) : 0.23000
REMARK 3 B33 (A**2) : 0.12000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.03000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.038
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.035
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.020
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.910
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 853 ; 0.006 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 591 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1156 ; 1.227 ; 1.942
REMARK 3 BOND ANGLES OTHERS (DEGREES): 1431 ; 0.744 ; 3.003
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 98 ; 6.909 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 45 ;33.353 ;24.000
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 148 ;11.286 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;21.752 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 120 ; 0.080 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 939 ; 0.004 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 180 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 132 ; 0.200 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 596 ; 0.195 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 399 ; 0.175 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): 467 ; 0.084 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 67 ; 0.139 ; 0.200
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): 7 ; 0.207 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 30 ; 0.142 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.150 ; 0.200
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): 646 ; 1.187 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 195 ; 0.302 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 812 ; 1.369 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 431 ; 1.978 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 344 ; 2.541 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1836 ; 2.029 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): 91 ; 2.980 ; 3.000
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1420 ; 1.845 ; 3.000
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 : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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 2YXF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-APR-07.
REMARK 100 THE DEPOSITION ID IS D_1000027255.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-DEC-05
REMARK 200 TEMPERATURE (KELVIN) : 90.0
REMARK 200 PH : 7.00
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL44XU
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.65
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : BRUKER DIP-6040
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38852
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.130
REMARK 200 RESOLUTION RANGE LOW (A) : 26.630
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 3.800
REMARK 200 R MERGE (I) : 0.05100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.70
REMARK 200 R MERGE FOR SHELL (I) : 0.33200
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 2D4F
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 43.78
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4000, 25% GLYCEROL, 0.06M
REMARK 280 AMMONIUMACETATE, 0.1M MOPS, PH 7.00, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 288K
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 38.82200
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.45350
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.82200
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.45350
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 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 SER A 57 -91.98 -105.61
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2D4F RELATED DB: PDB
REMARK 900 THE SAME PROTEIN AT 1.7A RESOLUTION
DBREF 2YXF A 1 99 UNP P61769 B2MG_HUMAN 21 119
SEQADV 2YXF MET A 0 UNP P61769 EXPRESSION TAG
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
FORMUL 2 HOH *91(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 ASP A 53 O LEU A 65
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 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 -3.05
CRYST1 77.644 28.907 54.397 90.00 121.59 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 0.012879 0.000000 0.007920 0.00000
SCALE2 0.000000 0.034593 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021581 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
