HEADER CYTOKINE 09-MAY-21 7MRV TITLE F100A MUTANT STRUCTURE OF MIF2 (D-DT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-DOPACHROME DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: D-DOPACHROME TAUTOMERASE,PHENYLPYRUVATE TAUTOMERASE II; COMPND 5 EC: 4.1.1.84; COMPND 6 ENGINEERED: YES; COMPND 7 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: DDT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR E.L.MURPHY,R.MANJULA,J.W.MURPHY,E.LOLIS REVDAT 4 18-OCT-23 7MRV 1 REMARK REVDAT 3 08-SEP-21 7MRV 1 JRNL REVDAT 2 25-AUG-21 7MRV 1 JRNL REVDAT 1 18-AUG-21 7MRV 0 JRNL AUTH E.CHEN,K.REISS,D.SHAH,R.MANJULA,B.ALLEN,E.L.MURPHY, JRNL AUTH 2 J.W.MURPHY,V.S.BATISTA,V.BHANDARI,E.J.LOLIS,G.P.LISI JRNL TITL A STRUCTURALLY PRESERVED ALLOSTERIC SITE IN THE MIF JRNL TITL 2 SUPERFAMILY AFFECTS ENZYMATIC ACTIVITY AND CD74 ACTIVATION JRNL TITL 3 IN D-DOPACHROME TAUTOMERASE. JRNL REF J.BIOL.CHEM. V. 297 01061 2021 JRNL REFN ESSN 1083-351X JRNL PMID 34384784 JRNL DOI 10.1016/J.JBC.2021.101061 REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 13565 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 683 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 41.5800 - 2.6800 1.00 2562 168 0.1490 0.1991 REMARK 3 2 2.6800 - 2.1300 1.00 2599 116 0.1798 0.2168 REMARK 3 3 2.1300 - 1.8600 1.00 2604 121 0.1757 0.2022 REMARK 3 4 1.8600 - 1.6900 1.00 2573 142 0.1653 0.2288 REMARK 3 5 1.6900 - 1.5700 0.98 2544 136 0.2065 0.2616 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.91 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7MRV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000256726. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.514 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC VARIMAX ARCSEC CU-HF REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13566 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.12900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3KAN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 25% PEG3350, REMARK 280 0.1M TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 41.58050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.00651 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 12.59367 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 41.58050 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 24.00651 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 12.59367 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 41.58050 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 24.00651 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 12.59367 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.01303 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 25.18733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 48.01303 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 25.18733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 48.01303 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 25.18733 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: 6650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 KCAL/MOL 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 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 ILE A 110 REMARK 465 GLY A 111 REMARK 465 THR A 112 REMARK 465 VAL A 113 REMARK 465 MET A 114 REMARK 465 THR A 115 REMARK 465 PHE A 116 REMARK 465 LEU A 117 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 ARG A 13 CZ NH1 NH2 REMARK 470 LYS A 20 CD CE NZ REMARK 470 ARG A 36 CD NE CZ NH1 NH2 REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 ARG A 74 NE CZ NH1 NH2 REMARK 470 LYS A 86 CE NZ REMARK 470 GLN A 92 CD OE1 NE2 REMARK 470 LYS A 109 CG CD CE NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 DBREF 7MRV A 1 117 UNP P30046 DOPD_HUMAN 2 118 SEQADV 7MRV ALA A 100 UNP P30046 PHE 101 ENGINEERED MUTATION SEQRES 1 A 117 PRO PHE LEU GLU LEU ASP THR ASN LEU PRO ALA ASN ARG SEQRES 2 A 117 VAL PRO ALA GLY LEU GLU LYS ARG LEU CYS ALA ALA ALA SEQRES 3 A 117 ALA SER ILE LEU GLY LYS PRO ALA ASP ARG VAL ASN VAL SEQRES 4 A 117 THR VAL ARG PRO GLY LEU ALA MET ALA LEU SER GLY SER SEQRES 5 A 117 THR GLU PRO CYS ALA GLN LEU SER ILE SER SER ILE GLY SEQRES 6 A 117 VAL VAL GLY THR ALA GLU ASP ASN ARG SER HIS SER ALA SEQRES 7 A 117 HIS PHE PHE GLU PHE LEU THR LYS GLU LEU ALA LEU GLY SEQRES 8 A 117 GLN ASP ARG ILE LEU ILE ARG PHE ALA PRO LEU GLU SER SEQRES 9 A 117 TRP GLN ILE GLY LYS ILE GLY THR VAL MET THR PHE LEU HET SO4 A 201 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *137(H2 O) HELIX 1 AA1 PRO A 10 VAL A 14 5 5 HELIX 2 AA2 GLY A 17 GLY A 31 1 15 HELIX 3 AA3 PRO A 33 VAL A 37 5 5 HELIX 4 AA4 THR A 69 ALA A 89 1 21 HELIX 5 AA5 GLY A 91 ASP A 93 5 3 SHEET 1 AA1 4 ASN A 38 ARG A 42 0 SHEET 2 AA1 4 PHE A 2 THR A 7 1 N LEU A 5 O ARG A 42 SHEET 3 AA1 4 ALA A 57 SER A 63 -1 O SER A 60 N GLU A 4 SHEET 4 AA1 4 ILE A 95 PRO A 101 1 O LEU A 96 N LEU A 59 SITE 1 AC1 6 PRO A 1 SER A 63 ILE A 64 TRP A 105 SITE 2 AC1 6 HOH A 302 HOH A 327 CRYST1 83.161 83.161 37.781 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 0.012025 0.006943 0.000000 0.00000 SCALE2 0.000000 0.013885 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026468 0.00000