HEADER CYTOKINE 12-SEP-24 9JIT TITLE MACROPHAGE MIGRATION INHIBITORY FACTOR S61H/Y100H MUTANT TITLE 2 (MIF(S61H/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 9JIT 1 JRNL REVDAT 1 06-AUG-25 9JIT 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. 1.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 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) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 171519 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) : 0.138 REMARK 3 FREE R VALUE : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 8439 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) : 1.08 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.11 REMARK 3 REFLECTION IN BIN (WORKING SET) : 11947 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1780 REMARK 3 BIN FREE R VALUE SET COUNT : 610 REMARK 3 BIN FREE R VALUE : 0.1950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2607 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 527 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01700 REMARK 3 B22 (A**2) : 0.02700 REMARK 3 B33 (A**2) : -0.01000 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): 0.024 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.024 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.014 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.628 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2814 ; 0.016 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2636 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3848 ; 1.826 ; 1.782 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6062 ; 0.650 ; 1.725 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 365 ; 5.965 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 15 ; 6.611 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 427 ;10.406 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 431 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3404 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 654 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 502 ; 0.240 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 33 ; 0.211 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1378 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 325 ; 0.257 ; 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): 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): 1430 ; 7.204 ; 1.289 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1430 ; 7.203 ; 1.288 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1805 ; 6.130 ; 2.319 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1806 ; 6.128 ; 2.319 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1384 ; 7.670 ; 1.575 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1385 ; 7.668 ; 1.575 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2043 ; 9.692 ; 2.766 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2044 ; 9.689 ; 2.767 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): 5450 ; 4.840 ; 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 9JIT 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_1300051432. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-21 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 : BL45XU 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 EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 171618 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.080 REMARK 200 RESOLUTION RANGE LOW (A) : 48.031 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.68400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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 (%): 53.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 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 33.89450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.38550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.96600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.38550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.89450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.96600 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: 8670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 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 C 431 O HOH C 441 1.73 REMARK 500 O HOH C 354 O HOH C 410 1.74 REMARK 500 O HOH A 308 O HOH A 406 1.77 REMARK 500 O HOH A 412 O HOH C 398 1.85 REMARK 500 O HOH A 313 O HOH A 386 1.90 REMARK 500 O HOH C 340 O HOH C 419 1.90 REMARK 500 O HOH A 327 O HOH A 374 1.91 REMARK 500 O HOH B 414 O HOH B 474 1.93 REMARK 500 O HOH B 422 O HOH B 429 1.97 REMARK 500 O HOH A 312 O HOH A 331 1.97 REMARK 500 O HOH C 342 O HOH C 433 1.97 REMARK 500 O HOH A 391 O HOH C 413 1.98 REMARK 500 CD1 ILE B 5 O HOH B 301 1.98 REMARK 500 O HOH C 379 O HOH C 456 2.00 REMARK 500 O HOH B 337 O HOH B 386 2.03 REMARK 500 O HOH B 429 O HOH B 465 2.04 REMARK 500 OD1 ASN C 103 O HOH C 301 2.06 REMARK 500 O HOH A 392 O HOH B 305 2.07 REMARK 500 OD1 ASN B 7 O HOH B 301 2.09 REMARK 500 O HOH A 410 O HOH B 326 2.15 REMARK 500 O HOH B 408 O HOH B 462 2.17 REMARK 500 O HOH B 326 O HOH B 486 2.18 REMARK 500 O HOH B 343 O HOH B 486 2.19 REMARK 500 O HOH C 402 O HOH C 447 2.19 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 319 O HOH C 317 4455 1.36 REMARK 500 O HOH B 438 O HOH C 438 3454 1.85 REMARK 500 O HOH A 386 O HOH C 405 3454 1.96 REMARK 500 O HOH B 447 O HOH C 403 2454 2.00 REMARK 500 O HOH A 302 O HOH C 476 4455 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 MET B 48 SD MET B 48 CE -0.365 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 B 3 CG - SD - CE ANGL. DEV. = -30.0 DEGREES REMARK 500 MET B 48 CG - SD - CE ANGL. DEV. = -14.5 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 -157.21 -148.61 REMARK 500 SER B 112 -159.74 -149.23 REMARK 500 SER C 112 -159.13 -149.21 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 A 12 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 502 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH B 503 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH B 504 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH B 505 DISTANCE = 7.69 ANGSTROMS REMARK 525 HOH B 506 DISTANCE = 8.81 ANGSTROMS REMARK 525 HOH C 479 DISTANCE = 6.74 ANGSTROMS DBREF 9JIT A 1 115 UNP P14174 MIF_HUMAN 1 115 DBREF 9JIT B 1 115 UNP P14174 MIF_HUMAN 1 115 DBREF 9JIT C 1 115 UNP P14174 MIF_HUMAN 1 115 SEQADV 9JIT HIS A 61 UNP P14174 SER 61 ENGINEERED MUTATION SEQADV 9JIT HIS A 100 UNP P14174 TYR 100 ENGINEERED MUTATION SEQADV 9JIT HIS B 61 UNP P14174 SER 61 ENGINEERED MUTATION SEQADV 9JIT HIS B 100 UNP P14174 TYR 100 ENGINEERED MUTATION SEQADV 9JIT HIS C 61 UNP P14174 SER 61 ENGINEERED MUTATION SEQADV 9JIT 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 HIS 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 HIS 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 HIS 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 SO4 A 201 5 HET GOL A 202 6 HET IPA A 203 4 HET SO4 B 201 5 HET SO4 B 202 5 HET GOL B 203 6 HET IPA B 204 4 HET SO4 C 201 5 HET GOL C 202 6 HET IPA C 203 4 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 SO4 4(O4 S 2-) FORMUL 5 GOL 3(C3 H8 O3) FORMUL 6 IPA 3(C3 H8 O) FORMUL 14 HOH *527(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 42 O LEU B 47 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 HIS A 63 N MET A 3 SHEET 5 AA1 7 VAL A 95 ASP A 101 1 O ASN A 98 N LEU A 62 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 42 N LEU A 47 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 HIS C 63 N MET C 3 SHEET 5 AA2 7 VAL C 95 ASP C 101 1 O ASN C 98 N LEU C 62 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 LEU B 62 O ASN B 98 SHEET 5 AA3 7 MET B 3 THR B 8 -1 N MET B 3 O HIS B 63 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 CRYST1 67.789 67.932 86.771 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 0.014752 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014721 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011525 0.00000 CONECT 2702 2703 2704 2705 2706 CONECT 2703 2702 CONECT 2704 2702 CONECT 2705 2702 CONECT 2706 2702 CONECT 2707 2708 2709 CONECT 2708 2707 CONECT 2709 2707 2710 2711 CONECT 2710 2709 CONECT 2711 2709 2712 CONECT 2712 2711 CONECT 2713 2714 CONECT 2714 2713 2715 2716 CONECT 2715 2714 CONECT 2716 2714 CONECT 2717 2718 2719 2720 2721 CONECT 2718 2717 CONECT 2719 2717 CONECT 2720 2717 CONECT 2721 2717 CONECT 2722 2723 2724 2725 2726 CONECT 2723 2722 CONECT 2724 2722 CONECT 2725 2722 CONECT 2726 2722 CONECT 2727 2728 2729 CONECT 2728 2727 CONECT 2729 2727 2730 2731 CONECT 2730 2729 CONECT 2731 2729 2732 CONECT 2732 2731 CONECT 2733 2734 CONECT 2734 2733 2735 2736 CONECT 2735 2734 CONECT 2736 2734 CONECT 2737 2738 2739 2740 2741 CONECT 2738 2737 CONECT 2739 2737 CONECT 2740 2737 CONECT 2741 2737 CONECT 2742 2743 2744 CONECT 2743 2742 CONECT 2744 2742 2745 2746 CONECT 2745 2744 CONECT 2746 2744 2747 CONECT 2747 2746 CONECT 2748 2749 CONECT 2749 2748 2750 2751 CONECT 2750 2749 CONECT 2751 2749 MASTER 399 0 10 18 21 0 0 6 3184 3 50 27 END