PDB Short entry for 1CGQ HEADER PROTEIN HORMONE 25-MAR-99 1CGQ TITLE MACROPHAGE MIGRATION INHIBITORY FACTOR (MIF) WITH ALANINE INSERTED TITLE 2 BETWEEN PRO-1 AND MET-2 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 3 27-DEC-23 1CGQ 1 SEQADV REVDAT 2 24-FEB-09 1CGQ 1 VERSN REVDAT 1 07-JUN-99 1CGQ 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. 2.00 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) : 2.00 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) (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 27635 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) : 0.234 REMARK 3 FREE R VALUE : 0.275 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 : 2616 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 111 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.510 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 1CGQ 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_1000000722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-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 : 43495 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 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 (%): 55.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 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 33.90500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.38500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.93500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.38500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.90500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.93500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG C 88 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES 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 SER A 111 -157.26 -150.50 REMARK 500 SER B 111 -157.88 -148.60 REMARK 500 SER C 111 -156.84 -150.24 REMARK 500 REMARK 500 REMARK: NULL DBREF 1CGQ A 0 114 UNP P14174 MIF_HUMAN 2 115 DBREF 1CGQ B 0 114 UNP P14174 MIF_HUMAN 2 115 DBREF 1CGQ C 0 114 UNP P14174 MIF_HUMAN 2 115 SEQADV 1CGQ ALA A 1 UNP P14174 INSERTION SEQADV 1CGQ ALA B 1 UNP P14174 INSERTION SEQADV 1CGQ ALA C 1 UNP P14174 INSERTION SEQRES 1 A 115 PRO ALA MET PHE ILE VAL ASN THR ASN VAL PRO ARG ALA SEQRES 2 A 115 SER VAL PRO ASP GLY PHE LEU SER GLU LEU THR GLN GLN SEQRES 3 A 115 LEU ALA GLN ALA THR GLY LYS PRO PRO GLN TYR ILE ALA SEQRES 4 A 115 VAL HIS VAL VAL PRO ASP GLN LEU MET ALA PHE GLY GLY SEQRES 5 A 115 SER SER GLU PRO CYS ALA LEU CYS SER LEU HIS SER ILE SEQRES 6 A 115 GLY LYS ILE GLY GLY ALA GLN ASN ARG SER TYR SER LYS SEQRES 7 A 115 LEU LEU CYS GLY LEU LEU ALA GLU ARG LEU ARG ILE SER SEQRES 8 A 115 PRO ASP ARG VAL TYR ILE ASN TYR TYR ASP MET ASN ALA SEQRES 9 A 115 ALA ASN VAL GLY TRP ASN ASN SER THR PHE ALA SEQRES 1 B 115 PRO ALA MET PHE ILE VAL ASN THR ASN VAL PRO ARG ALA SEQRES 2 B 115 SER VAL PRO ASP GLY PHE LEU SER GLU LEU THR GLN GLN SEQRES 3 B 115 LEU ALA GLN ALA THR GLY LYS PRO PRO GLN TYR ILE ALA SEQRES 4 B 115 VAL HIS VAL VAL PRO ASP GLN LEU MET ALA PHE GLY GLY SEQRES 5 B 115 SER SER GLU PRO CYS ALA LEU CYS SER LEU HIS SER ILE SEQRES 6 B 115 GLY LYS ILE GLY GLY ALA GLN ASN ARG SER TYR SER LYS SEQRES 7 B 115 LEU LEU CYS GLY LEU LEU ALA GLU ARG LEU ARG ILE SER SEQRES 8 B 115 PRO ASP ARG VAL TYR ILE ASN TYR TYR ASP MET ASN ALA SEQRES 9 B 115 ALA ASN VAL GLY TRP ASN ASN SER THR PHE ALA SEQRES 1 C 115 PRO ALA MET PHE ILE VAL ASN THR ASN VAL PRO ARG ALA SEQRES 2 C 115 SER VAL PRO ASP GLY PHE LEU SER GLU LEU THR GLN GLN SEQRES 3 C 115 LEU ALA GLN ALA THR GLY LYS PRO PRO GLN TYR ILE ALA SEQRES 4 C 115 VAL HIS VAL VAL PRO ASP GLN LEU MET ALA PHE GLY GLY SEQRES 5 C 115 SER SER GLU PRO CYS ALA LEU CYS SER LEU HIS SER ILE SEQRES 6 C 115 GLY LYS ILE GLY GLY ALA GLN ASN ARG SER TYR SER LYS SEQRES 7 C 115 LEU LEU CYS GLY LEU LEU ALA GLU ARG LEU ARG ILE SER SEQRES 8 C 115 PRO ASP ARG VAL TYR ILE ASN TYR TYR ASP MET ASN ALA SEQRES 9 C 115 ALA ASN VAL GLY TRP ASN ASN SER THR PHE ALA FORMUL 4 HOH *111(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 67.810 67.870 88.770 90.00 90.00 90.00 P 21 21 21 12 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 0.014747 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014734 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011265 0.00000 MTRIX1 1 0.022017 -0.999749 0.004246 -5.28540 1 MTRIX2 1 -0.029297 0.003600 0.999564 -82.40800 1 MTRIX3 1 -0.999328 -0.022132 -0.029210 79.75200 1 MTRIX1 2 0.022211 -0.021420 -0.999524 77.60990 1 MTRIX2 2 -0.999709 0.008982 -0.022408 -3.04000 1 MTRIX3 2 0.009458 0.999730 -0.021214 84.25880 1