HEADER PROTEIN HORMONE 24-MAR-99 1P1G
TITLE MACROPHAGE MIGRATION INHIBITORY FACTOR (MIF) WITH PRO-1 MUTATED TO
TITLE 2 GLY-1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN (MACROPHAGE MIGRATION INHIBITORY FACTOR);
COMPND 3 CHAIN: A, B, C;
COMPND 4 SYNONYM: MIF;
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 STRAIN: BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-11B
KEYWDS PROTEIN HORMONE, CYTOKINE, ENZYME
EXPDTA X-RAY DIFFRACTION
AUTHOR J.B.LUBETSKY,E.LOLIS
REVDAT 4 27-DEC-23 1P1G 1 SEQADV
REVDAT 3 14-MAR-18 1P1G 1 SEQADV
REVDAT 2 24-FEB-09 1P1G 1 VERSN
REVDAT 1 07-JUN-99 1P1G 0
JRNL AUTH J.B.LUBETSKY,M.SWOPE,C.DEALWIS,P.BLAKE,E.LOLIS
JRNL TITL PRO-1 OF MACROPHAGE MIGRATION INHIBITORY FACTOR FUNCTIONS AS
JRNL TITL 2 A CATALYTIC BASE IN THE PHENYLPYRUVATE TAUTOMERASE ACTIVITY.
JRNL REF BIOCHEMISTRY V. 38 7346 1999
JRNL REFN ISSN 0006-2960
JRNL PMID 10353846
JRNL DOI 10.1021/BI990306M
REMARK 2
REMARK 2 RESOLUTION. 2.50 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.7
REMARK 3 NUMBER OF REFLECTIONS : 18017
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) : 0.227
REMARK 3 FREE R VALUE : 0.270
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
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) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
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 : 2592
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 33
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 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.550
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 NCS MODEL : RESTRAINTS
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 PARAMETER FILE 2 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 2 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1P1G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-99.
REMARK 100 THE DEPOSITION ID IS D_1000000716.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : DEC-97
REMARK 200 TEMPERATURE (KELVIN) : 133
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10598
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7
REMARK 200 DATA REDUNDANCY : 1.700
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.04900
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8
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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 67.05
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.73
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+2/3
REMARK 290 6555 -X,-X+Y,-Z+1/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.72000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 69.44000
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 69.44000
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.72000
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 6730 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 13140 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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
DBREF 1P1G A 1 114 UNP P14174 MIF_HUMAN 2 115
DBREF 1P1G B 1 114 UNP P14174 MIF_HUMAN 2 115
DBREF 1P1G C 1 114 UNP P14174 MIF_HUMAN 2 115
SEQADV 1P1G GLY A 1 UNP P14174 PRO 2 ENGINEERED MUTATION
SEQADV 1P1G GLY B 1 UNP P14174 PRO 2 ENGINEERED MUTATION
SEQADV 1P1G GLY C 1 UNP P14174 PRO 2 ENGINEERED MUTATION
SEQRES 1 A 114 GLY MET PHE ILE VAL ASN THR ASN VAL PRO ARG ALA SER
SEQRES 2 A 114 VAL PRO ASP GLY PHE LEU SER GLU LEU THR GLN GLN LEU
SEQRES 3 A 114 ALA GLN ALA THR GLY LYS PRO PRO GLN TYR ILE ALA VAL
SEQRES 4 A 114 HIS VAL VAL PRO ASP GLN LEU MET ALA PHE GLY GLY SER
SEQRES 5 A 114 SER GLU PRO CYS ALA LEU CYS SER LEU HIS SER ILE GLY
SEQRES 6 A 114 LYS ILE GLY GLY ALA GLN ASN ARG SER TYR SER LYS LEU
SEQRES 7 A 114 LEU CYS GLY LEU LEU ALA GLU ARG LEU ARG ILE SER PRO
SEQRES 8 A 114 ASP ARG VAL TYR ILE ASN TYR TYR ASP MET ASN ALA ALA
SEQRES 9 A 114 ASN VAL GLY TRP ASN ASN SER THR PHE ALA
SEQRES 1 B 114 GLY MET PHE ILE VAL ASN THR ASN VAL PRO ARG ALA SER
SEQRES 2 B 114 VAL PRO ASP GLY PHE LEU SER GLU LEU THR GLN GLN LEU
SEQRES 3 B 114 ALA GLN ALA THR GLY LYS PRO PRO GLN TYR ILE ALA VAL
SEQRES 4 B 114 HIS VAL VAL PRO ASP GLN LEU MET ALA PHE GLY GLY SER
SEQRES 5 B 114 SER GLU PRO CYS ALA LEU CYS SER LEU HIS SER ILE GLY
SEQRES 6 B 114 LYS ILE GLY GLY ALA GLN ASN ARG SER TYR SER LYS LEU
SEQRES 7 B 114 LEU CYS GLY LEU LEU ALA GLU ARG LEU ARG ILE SER PRO
SEQRES 8 B 114 ASP ARG VAL TYR ILE ASN TYR TYR ASP MET ASN ALA ALA
SEQRES 9 B 114 ASN VAL GLY TRP ASN ASN SER THR PHE ALA
SEQRES 1 C 114 GLY MET PHE ILE VAL ASN THR ASN VAL PRO ARG ALA SER
SEQRES 2 C 114 VAL PRO ASP GLY PHE LEU SER GLU LEU THR GLN GLN LEU
SEQRES 3 C 114 ALA GLN ALA THR GLY LYS PRO PRO GLN TYR ILE ALA VAL
SEQRES 4 C 114 HIS VAL VAL PRO ASP GLN LEU MET ALA PHE GLY GLY SER
SEQRES 5 C 114 SER GLU PRO CYS ALA LEU CYS SER LEU HIS SER ILE GLY
SEQRES 6 C 114 LYS ILE GLY GLY ALA GLN ASN ARG SER TYR SER LYS LEU
SEQRES 7 C 114 LEU CYS GLY LEU LEU ALA GLU ARG LEU ARG ILE SER PRO
SEQRES 8 C 114 ASP ARG VAL TYR ILE ASN TYR TYR ASP MET ASN ALA ALA
SEQRES 9 C 114 ASN VAL GLY TRP ASN ASN SER THR PHE ALA
FORMUL 4 HOH *33(H2 O)
HELIX 1 1 PHE A 18 THR A 30 1 13
HELIX 2 2 GLY A 69 ARG A 88 1 20
HELIX 3 3 PHE B 18 THR B 30 1 13
HELIX 4 4 GLY B 69 ARG B 88 1 20
HELIX 5 5 PHE C 18 THR C 30 1 13
HELIX 6 6 GLY C 69 ARG C 88 1 20
SHEET 1 A 4 ALA A 38 VAL A 42 0
SHEET 2 A 4 MET A 2 THR A 7 1
SHEET 3 A 4 PRO A 55 SER A 63 -1
SHEET 4 A 4 TYR A 95 MET A 101 1
SHEET 1 B 4 ALA B 38 VAL B 42 0
SHEET 2 B 4 MET B 2 THR B 7 1
SHEET 3 B 4 PRO B 55 SER B 63 -1
SHEET 4 B 4 TYR B 95 MET B 101 1
SHEET 1 C 4 ALA C 38 VAL C 42 0
SHEET 2 C 4 MET C 2 THR C 7 1
SHEET 3 C 4 PRO C 55 SER C 63 -1
SHEET 4 C 4 TYR C 95 MET C 101 1
CRYST1 95.810 95.810 104.160 90.00 90.00 120.00 P 31 2 1 18
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 0.010437 0.006026 0.000000 0.00000
SCALE2 0.000000 0.012052 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009601 0.00000
MTRIX1 1 0.239030 -0.308027 0.920861 -9.89960 1
MTRIX2 1 -0.962488 0.050222 0.266634 2.43200 1
MTRIX3 1 -0.128377 -0.950051 -0.284468 21.94220 1
MTRIX1 2 0.249850 -0.960240 -0.124554 7.66630 1
MTRIX2 2 -0.310158 0.042490 -0.949735 17.89990 1
MTRIX3 2 0.917266 0.275923 -0.287210 14.25640 1
(ATOM LINES ARE NOT SHOWN.)
END
