HEADER CYTOKINE 27-OCT-07 3B64 TITLE MACROPHAGE MIGRATION INHIBITORY FACTOR (MIF) FROM /LEISHMANIA MAJOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE MIGRATION INHIBITORY FACTOR-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 4 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 5 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PCRT7/CT-TOPO KEYWDS CYTOKINE, LEISHMANIA, MACROPHAGE MIGRATION INHIBITORY FACTOR, MIF, KEYWDS 2 LM1740MIF, LMMIF, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR S.ZIEROW,Y.CHO,E.LOLIS REVDAT 3 21-FEB-24 3B64 1 REMARK REVDAT 2 24-FEB-09 3B64 1 VERSN REVDAT 1 10-JUN-08 3B64 0 JRNL AUTH D.KAMIR,S.ZIEROW,L.LENG,Y.CHO,Y.DIAZ,J.GRIFFITH,C.MCDONALD, JRNL AUTH 2 M.MERK,R.A.MITCHELL,J.TRENT,Y.CHEN,Y.K.KWONG,H.XIONG, JRNL AUTH 3 J.VERMEIRE,M.CAPPELLO,D.MCMAHON-PRATT,J.WALKER,J.BERNHAGEN, JRNL AUTH 4 E.LOLIS,R.BUCALA JRNL TITL A LEISHMANIA ORTHOLOG OF MACROPHAGE MIGRATION INHIBITORY JRNL TITL 2 FACTOR MODULATES HOST MACROPHAGE RESPONSES. JRNL REF J.IMMUNOL. V. 180 8250 2008 JRNL REFN ISSN 0022-1767 JRNL PMID 18523291 REMARK 2 REMARK 2 RESOLUTION. 1.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.139 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.133 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2334 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 44388 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.133 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.127 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2033 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 38792 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 867 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 985.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 13 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 9061 REMARK 3 NUMBER OF RESTRAINTS : 11105 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.097 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.092 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.034 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.032 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.093 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY ? REMARK 4 REMARK 4 3B64 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045125. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46731 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.030 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.22800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES-NA, 20% (V/V) ISO-PROPANO REMARK 280 POLYETHYLENE GLYCOL 4000, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.16050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.10377 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.27233 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 26.16050 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 15.10377 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.27233 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 26.16050 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 15.10377 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.27233 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.20754 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 64.54467 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 30.20754 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 64.54467 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 30.20754 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 64.54467 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: 7410 ANGSTROM**2 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 26.16050 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 45.31132 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -26.16050 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 45.31132 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 4 CG CD OE1 NE2 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 A 16 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 16 NE - CZ - NH2 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 28 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 PHE A 51 CB - CG - CD1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 61 CD - NE - CZ ANGL. DEV. = -9.5 DEGREES REMARK 500 ARG A 61 NH1 - CZ - NH2 ANGL. DEV. = -9.5 DEGREES REMARK 500 ARG A 61 NE - CZ - NH2 ANGL. DEV. = 8.6 DEGREES REMARK 500 GLU A 74 OE1 - CD - OE2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ASP A 93 CB - CG - OD1 ANGL. DEV. = -7.8 DEGREES REMARK 500 PHE A 96 CB - CG - CD2 ANGL. DEV. = 4.5 DEGREES REMARK 500 PHE A 96 CB - CG - CD1 ANGL. DEV. = -4.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 113 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MIF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE AT 2.6-A RESOLUTION OF HUMAN MACROPHAGE MIGRATION REMARK 900 INHIBITORY FACTOR. REMARK 900 RELATED ID: 2OS5 RELATED DB: PDB REMARK 900 STRUCTURAL CHARACTERIZATION OF A MACROPHAGE MIGRATION INHIBITORY REMARK 900 FACTOR FROM ANCYLOSTOMA HOOKWORMS: EVIDENCE FOR INTERACTION WITH REMARK 900 HUMAN MIF RECEPTOR CD74 DBREF 3B64 A 1 112 UNP Q4Q413 Q4Q413_LEIMA 2 113 SEQRES 1 A 112 PRO VAL ILE GLN THR PHE VAL SER THR PRO LEU ASP HIS SEQRES 2 A 112 HIS LYS ARG GLU ASN LEU ALA GLN VAL TYR ARG ALA VAL SEQRES 3 A 112 THR ARG ASP VAL LEU GLY LYS PRO GLU ASP LEU VAL MET SEQRES 4 A 112 MET THR PHE HIS ASP SER THR PRO MET HIS PHE PHE GLY SEQRES 5 A 112 SER THR ASP PRO VAL ALA CYS VAL ARG VAL GLU ALA LEU SEQRES 6 A 112 GLY GLY TYR GLY PRO SER GLU PRO GLU LYS VAL THR SER SEQRES 7 A 112 ILE VAL THR ALA ALA ILE THR LYS GLU CYS GLY ILE VAL SEQRES 8 A 112 ALA ASP ARG ILE PHE VAL LEU TYR PHE SER PRO LEU HIS SEQRES 9 A 112 CYS GLY TRP ASN GLY THR ASN PHE HET IPA A 113 4 HETNAM IPA ISOPROPYL ALCOHOL HETSYN IPA 2-PROPANOL FORMUL 2 IPA C3 H8 O FORMUL 3 HOH *120(H2 O) HELIX 1 1 ASP A 12 VAL A 30 1 19 HELIX 2 2 PRO A 34 VAL A 38 5 5 HELIX 3 3 SER A 71 GLY A 89 1 19 HELIX 4 4 VAL A 91 ASP A 93 5 3 SHEET 1 A 4 MET A 39 HIS A 43 0 SHEET 2 A 4 VAL A 2 VAL A 7 1 N THR A 5 O HIS A 43 SHEET 3 A 4 ALA A 58 GLU A 63 -1 O ARG A 61 N GLN A 4 SHEET 4 A 4 ILE A 95 PHE A 100 1 O LEU A 98 N VAL A 62 SHEET 1 B 2 GLY A 106 TRP A 107 0 SHEET 2 B 2 THR A 110 ASN A 111 -1 O THR A 110 N TRP A 107 SITE 1 AC1 4 TRP A 107 THR A 110 ASN A 111 PHE A 112 CRYST1 52.321 52.321 96.817 90.00 90.00 120.00 H 3 9 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 0.019113 0.011035 0.000000 0.00000 SCALE2 0.000000 0.022070 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010329 0.00000