HEADER CYTOKINE 12-SEP-24 9JJ0 TITLE MACROPHAGE MIGRATION INHIBITORY FACTOR Y100H MUTANT COMPLEXED WITH TITLE 2 THREE ZINC IONS (ZN3-MIF(Y100H)) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE MIGRATION INHIBITORY FACTOR; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: MIF,GLYCOSYLATION-INHIBITING FACTOR,GIF,L-DOPACHROME COMPND 5 ISOMERASE,L-DOPACHROME TAUTOMERASE,PHENYLPYRUVATE TAUTOMERASE; COMPND 6 EC: 5.3.2.1,5.3.3.12; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MIF, GLIF, MMIF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MACROPHAGE MIGRATION INHIBITORY FACTOR, CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR T.HIMIYAMA,Y.OKAMOTO REVDAT 2 13-AUG-25 9JJ0 1 JRNL REVDAT 1 06-AUG-25 9JJ0 0 JRNL AUTH A.UENO,F.TAKIDA,T.KITA,T.ISHII,T.HIMIYAMA,T.MABUCHI, JRNL AUTH 2 Y.OKAMOTO JRNL TITL A CYTOKINE-BASED DESIGNER ENZYME WITH AN ABIOLOGICAL JRNL TITL 2 MULTINUCLEAR METAL CENTER EXHIBITS INTRINSIC AND EXTRINSIC JRNL TITL 3 CATALYSIS. JRNL REF NAT COMMUN V. 16 6781 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40745177 JRNL DOI 10.1038/S41467-025-61909-5 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 113094 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.118 REMARK 3 FREE R VALUE : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.926 REMARK 3 FREE R VALUE TEST SET COUNT : 5571 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) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7869 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 400 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2595 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 529 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.17100 REMARK 3 B22 (A**2) : -0.13900 REMARK 3 B33 (A**2) : -0.03100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.031 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.033 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.023 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.218 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.978 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2884 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2715 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3950 ; 1.806 ; 1.790 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6247 ; 0.664 ; 1.722 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 381 ; 5.671 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 16 ; 9.261 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 446 ;11.862 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 443 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3534 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 676 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 484 ; 0.244 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 37 ; 0.237 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1356 ; 0.174 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 369 ; 0.285 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 12 ; 0.101 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1473 ; 4.260 ; 1.754 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1473 ; 4.258 ; 1.754 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1871 ; 5.583 ; 3.161 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1872 ; 5.583 ; 3.161 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1411 ; 8.224 ; 2.100 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1412 ; 8.221 ; 2.102 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2079 ;11.004 ; 3.716 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2080 ;11.001 ; 3.717 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): 5599 ; 4.206 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : BABINET MODEL PLUS MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9JJ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1300051442. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-22 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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 113184 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 48.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.01700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, 20MM TRIS-HCL REMARK 280 BUFFER (PH 7.5), 3% ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 33.95300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.81450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.16000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.81450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.95300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.16000 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: 9420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -223.0 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 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 1 REMARK 465 MET B 1 REMARK 465 MET C 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 420 O HOH A 471 1.63 REMARK 500 O HOH A 317 O HOH B 302 1.71 REMARK 500 O HOH B 310 O HOH B 318 1.80 REMARK 500 OE1 GLN C 25 NE2 GLN C 29 1.80 REMARK 500 O HOH B 440 O HOH B 466 1.83 REMARK 500 O HOH A 419 O HOH C 309 1.85 REMARK 500 O HOH C 382 O HOH C 385 1.90 REMARK 500 O HOH A 344 O HOH A 434 1.90 REMARK 500 NH2 ARG B 74 O HOH B 301 1.92 REMARK 500 O HOH C 344 O HOH C 410 1.94 REMARK 500 O HOH C 349 O HOH C 453 1.94 REMARK 500 O HOH A 337 O HOH A 372 1.95 REMARK 500 O HOH B 335 O HOH B 454 1.95 REMARK 500 O HOH C 382 O HOH C 458 1.97 REMARK 500 O HOH A 466 O HOH A 472 1.98 REMARK 500 O HOH C 354 O HOH C 449 1.99 REMARK 500 O HOH A 339 O HOH A 426 2.01 REMARK 500 O HOH C 302 O HOH C 311 2.02 REMARK 500 O HOH B 406 O HOH B 434 2.02 REMARK 500 O HOH B 419 O HOH B 468 2.02 REMARK 500 O HOH A 347 O HOH A 417 2.03 REMARK 500 O HOH A 395 O HOH A 426 2.04 REMARK 500 O HOH B 395 O HOH B 463 2.05 REMARK 500 O HOH C 378 O HOH C 427 2.06 REMARK 500 O HOH A 309 O HOH A 332 2.08 REMARK 500 O HOH A 418 O HOH B 332 2.09 REMARK 500 O HOH C 455 O HOH C 466 2.11 REMARK 500 O HOH C 385 O HOH C 446 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 417 O HOH C 373 4445 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 MET A 3 CG - SD - CE ANGL. DEV. = -12.8 DEGREES REMARK 500 ARG A 74 CD - NE - CZ ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG A 74 NE - CZ - NH1 ANGL. DEV. = -5.1 DEGREES REMARK 500 LYS B 67 CD - CE - NZ ANGL. DEV. = -18.0 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 112 -154.88 -149.59 REMARK 500 SER B 112 -156.35 -150.00 REMARK 500 SER C 112 -157.34 -151.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 74 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 63 NE2 REMARK 620 2 CO3 A 204 O2 98.5 REMARK 620 3 HIS B 100 NE2 121.2 112.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 100 NE2 REMARK 620 2 CO3 A 204 O1 111.8 REMARK 620 3 HIS C 63 NE2 122.1 97.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CO3 A 204 O3 REMARK 620 2 HIS B 63 NE2 97.1 REMARK 620 3 HIS C 100 NE2 112.1 122.4 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9JIT RELATED DB: PDB-DEV DBREF 9JJ0 A 1 115 UNP P14174 MIF_HUMAN 1 115 DBREF 9JJ0 B 1 115 UNP P14174 MIF_HUMAN 1 115 DBREF 9JJ0 C 1 115 UNP P14174 MIF_HUMAN 1 115 SEQADV 9JJ0 HIS A 100 UNP P14174 TYR 100 ENGINEERED MUTATION SEQADV 9JJ0 HIS B 100 UNP P14174 TYR 100 ENGINEERED MUTATION SEQADV 9JJ0 HIS C 100 UNP P14174 TYR 100 ENGINEERED MUTATION SEQRES 1 A 115 MET PRO 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 HIS ASP MET ASN ALA SEQRES 9 A 115 ALA ASN VAL GLY TRP ASN ASN SER THR PHE ALA SEQRES 1 B 115 MET PRO 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 HIS ASP MET ASN ALA SEQRES 9 B 115 ALA ASN VAL GLY TRP ASN ASN SER THR PHE ALA SEQRES 1 C 115 MET PRO 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 HIS ASP MET ASN ALA SEQRES 9 C 115 ALA ASN VAL GLY TRP ASN ASN SER THR PHE ALA HET ZN A 201 1 HET ZN A 202 1 HET CL A 203 1 HET CO3 A 204 4 HET SO4 A 205 5 HET GOL A 206 6 HET IPA A 207 4 HET ZN B 201 1 HET CL B 202 1 HET SO4 B 203 5 HET GOL B 204 6 HET IPA B 205 4 HET CL C 201 1 HET SO4 C 202 5 HET GOL C 203 6 HET IPA C 204 4 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM CO3 CARBONATE ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM IPA ISOPROPYL ALCOHOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN IPA 2-PROPANOL FORMUL 4 ZN 3(ZN 2+) FORMUL 6 CL 3(CL 1-) FORMUL 7 CO3 C O3 2- FORMUL 8 SO4 3(O4 S 2-) FORMUL 9 GOL 3(C3 H8 O3) FORMUL 10 IPA 3(C3 H8 O) FORMUL 20 HOH *529(H2 O) HELIX 1 AA1 PRO A 11 VAL A 15 5 5 HELIX 2 AA2 GLY A 18 GLY A 32 1 15 HELIX 3 AA3 PRO A 34 TYR A 37 5 4 HELIX 4 AA4 GLY A 69 ARG A 89 1 21 HELIX 5 AA5 SER A 91 ASP A 93 5 3 HELIX 6 AA6 ASN A 103 ALA A 105 5 3 HELIX 7 AA7 PRO B 11 VAL B 15 5 5 HELIX 8 AA8 GLY B 18 GLY B 32 1 15 HELIX 9 AA9 PRO B 34 TYR B 37 5 4 HELIX 10 AB1 GLY B 69 ARG B 89 1 21 HELIX 11 AB2 SER B 91 ASP B 93 5 3 HELIX 12 AB3 ASN B 103 ALA B 105 5 3 HELIX 13 AB4 PRO C 11 VAL C 15 5 5 HELIX 14 AB5 GLY C 18 GLY C 32 1 15 HELIX 15 AB6 PRO C 34 TYR C 37 5 4 HELIX 16 AB7 GLY C 69 ARG C 89 1 21 HELIX 17 AB8 SER C 91 ASP C 93 5 3 HELIX 18 AB9 ASN C 103 ALA C 105 5 3 SHEET 1 AA1 7 LEU B 47 PHE B 50 0 SHEET 2 AA1 7 ALA A 39 VAL A 43 -1 N VAL A 40 O ALA B 49 SHEET 3 AA1 7 MET A 3 THR A 8 1 N VAL A 6 O VAL A 43 SHEET 4 AA1 7 ALA A 58 SER A 64 -1 O LEU A 59 N ASN A 7 SHEET 5 AA1 7 VAL A 95 ASP A 101 1 O TYR A 96 N CYS A 60 SHEET 6 AA1 7 VAL C 107 TRP C 109 -1 O GLY C 108 N ILE A 97 SHEET 7 AA1 7 SER C 112 THR C 113 -1 O SER C 112 N TRP C 109 SHEET 1 AA2 7 LEU A 47 PHE A 50 0 SHEET 2 AA2 7 ALA C 39 VAL C 43 -1 O VAL C 40 N ALA A 49 SHEET 3 AA2 7 MET C 3 THR C 8 1 N VAL C 6 O VAL C 43 SHEET 4 AA2 7 ALA C 58 SER C 64 -1 O LEU C 59 N ASN C 7 SHEET 5 AA2 7 VAL C 95 ASP C 101 1 O ASN C 98 N CYS C 60 SHEET 6 AA2 7 VAL B 107 TRP B 109 -1 N GLY B 108 O ILE C 97 SHEET 7 AA2 7 SER B 112 THR B 113 -1 O SER B 112 N TRP B 109 SHEET 1 AA3 7 SER A 112 THR A 113 0 SHEET 2 AA3 7 VAL A 107 TRP A 109 -1 N TRP A 109 O SER A 112 SHEET 3 AA3 7 VAL B 95 ASP B 101 -1 O ILE B 97 N GLY A 108 SHEET 4 AA3 7 ALA B 58 SER B 64 1 N CYS B 60 O TYR B 96 SHEET 5 AA3 7 MET B 3 THR B 8 -1 N ASN B 7 O LEU B 59 SHEET 6 AA3 7 ALA B 39 VAL B 43 1 O VAL B 43 N VAL B 6 SHEET 7 AA3 7 LEU C 47 PHE C 50 -1 O LEU C 47 N VAL B 42 LINK NE2 HIS A 63 ZN ZN A 201 1555 1555 2.04 LINK NE2 HIS A 100 ZN ZN A 202 1555 1555 2.01 LINK ZN ZN A 201 O2 CO3 A 204 1555 1555 1.92 LINK ZN ZN A 201 NE2 HIS B 100 1555 1555 2.04 LINK ZN ZN A 202 O1 CO3 A 204 1555 1555 1.95 LINK ZN ZN A 202 NE2 HIS C 63 1555 1555 2.02 LINK O3 CO3 A 204 ZN ZN B 201 1555 1555 1.97 LINK NE2 HIS B 63 ZN ZN B 201 1555 1555 2.00 LINK ZN ZN B 201 NE2 HIS C 100 1555 1555 1.95 CRYST1 67.906 68.320 87.629 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 0.014726 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014637 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011412 0.00000 CONECT 536 2769 CONECT 828 2770 CONECT 1439 2791 CONECT 1748 2769 CONECT 2362 2770 CONECT 2654 2791 CONECT 2769 536 1748 2774 CONECT 2770 828 2362 2773 CONECT 2772 2773 2774 2775 CONECT 2773 2770 2772 CONECT 2774 2769 2772 CONECT 2775 2772 2791 CONECT 2776 2777 2778 2779 2780 CONECT 2777 2776 CONECT 2778 2776 CONECT 2779 2776 CONECT 2780 2776 CONECT 2781 2782 2783 CONECT 2782 2781 CONECT 2783 2781 2784 2785 CONECT 2784 2783 CONECT 2785 2783 2786 CONECT 2786 2785 CONECT 2787 2788 CONECT 2788 2787 2789 2790 CONECT 2789 2788 CONECT 2790 2788 CONECT 2791 1439 2654 2775 CONECT 2793 2794 2795 2796 2797 CONECT 2794 2793 CONECT 2795 2793 CONECT 2796 2793 CONECT 2797 2793 CONECT 2798 2799 2800 CONECT 2799 2798 CONECT 2800 2798 2801 2802 CONECT 2801 2800 CONECT 2802 2800 2803 CONECT 2803 2802 CONECT 2804 2805 CONECT 2805 2804 2806 2807 CONECT 2806 2805 CONECT 2807 2805 CONECT 2809 2810 2811 2812 2813 CONECT 2810 2809 CONECT 2811 2809 CONECT 2812 2809 CONECT 2813 2809 CONECT 2814 2815 2816 CONECT 2815 2814 CONECT 2816 2814 2817 2818 CONECT 2817 2816 CONECT 2818 2816 2819 CONECT 2819 2818 CONECT 2820 2821 CONECT 2821 2820 2822 2823 CONECT 2822 2821 CONECT 2823 2821 MASTER 395 0 16 18 21 0 0 6 3179 3 58 27 END