HEADER CYTOKINE 15-MAY-21 7MW7 TITLE CRYSTAL STRUCTURE OF P1G MUTANT OF D-DOPACHROME TAUTOMERASE 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 MITOGEN INHIBITORY FACTOR 2, MUTANT, CYTOKINE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR R.MANJULA,E.L.MURPHY,J.W.MURPHY,E.LOLIS REVDAT 4 18-OCT-23 7MW7 1 REMARK REVDAT 3 08-SEP-21 7MW7 1 JRNL REMARK REVDAT 2 25-AUG-21 7MW7 1 JRNL REVDAT 1 18-AUG-21 7MW7 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. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3845 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 50146 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2501 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 34.5800 - 2.8700 1.00 2835 180 0.1636 0.1862 REMARK 3 2 2.8700 - 2.2800 1.00 2811 134 0.1785 0.1648 REMARK 3 3 2.2800 - 1.9900 1.00 2804 147 0.1717 0.1988 REMARK 3 4 1.9900 - 1.8100 1.00 2767 157 0.1809 0.1914 REMARK 3 5 1.8100 - 1.6800 1.00 2794 137 0.1773 0.2021 REMARK 3 6 1.6800 - 1.5800 1.00 2762 149 0.1836 0.1576 REMARK 3 7 1.5800 - 1.5000 1.00 2795 150 0.1794 0.2017 REMARK 3 8 1.5000 - 1.4400 1.00 2723 158 0.1977 0.1948 REMARK 3 9 1.4400 - 1.3800 1.00 2763 167 0.2014 0.2136 REMARK 3 10 1.3800 - 1.3300 1.00 2764 162 0.2039 0.2526 REMARK 3 11 1.3300 - 1.2900 1.00 2784 138 0.2001 0.2127 REMARK 3 12 1.2900 - 1.2500 1.00 2741 146 0.2024 0.1758 REMARK 3 13 1.2500 - 1.2200 1.00 2801 133 0.1999 0.2412 REMARK 3 14 1.2200 - 1.1900 1.00 2729 130 0.2126 0.2346 REMARK 3 15 1.1900 - 1.1600 0.98 2747 148 0.2110 0.2241 REMARK 3 16 1.1600 - 1.1400 0.91 2459 121 0.2172 0.2160 REMARK 3 17 1.1400 - 1.1200 0.74 2090 73 0.2196 0.2575 REMARK 3 18 1.1200 - 1.1000 0.53 1476 71 0.2311 0.2382 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) : 0.091 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.647 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.82 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 : 0.007 929 REMARK 3 ANGLE : 0.962 1267 REMARK 3 CHIRALITY : 0.080 149 REMARK 3 PLANARITY : 0.007 164 REMARK 3 DIHEDRAL : 6.471 134 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 7MW7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000256912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-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) : 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) : 1.51418 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 : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52539 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.090 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.38500 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: MOLREP REMARK 200 STARTING MODEL: 7MSE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M AMMONIUM SULFATE 0.1 M HEPES 7.5 REMARK 280 30 % V/V (+/-)-2-METHYL-2,4-PENTANEDIOL, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.53350 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 20.53350 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 20.53350 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: 7940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -137.0 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 -36.99650 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 64.07982 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -73.99300 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A 201 LIES ON A SPECIAL POSITION. REMARK 375 O4 SO4 A 201 LIES ON A SPECIAL POSITION. 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 NE CZ NH1 NH2 REMARK 470 LYS A 86 CE NZ REMARK 470 GLN A 92 CD OE1 NE2 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 ILE A 110 46.71 39.44 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 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SO4 A 201 O4 REMARK 620 2 SO4 A 201 O2 19.4 REMARK 620 3 SO4 A 201 O3 35.2 30.2 REMARK 620 4 SO4 A 201 O4 0.0 19.4 35.2 REMARK 620 5 HOH A 312 O 135.5 116.4 109.2 135.5 REMARK 620 6 HOH A 321 O 103.2 108.6 137.5 103.2 99.3 REMARK 620 7 HOH A 329 O 105.3 120.8 99.3 105.3 107.0 101.6 REMARK 620 N 1 2 3 4 5 6 DBREF 7MW7 A 0 117 UNP P30046 DOPD_HUMAN 1 118 SEQADV 7MW7 GLY A 1 UNP P30046 PRO 2 ENGINEERED MUTATION SEQRES 1 A 118 MET GLY PHE LEU GLU LEU ASP THR ASN LEU PRO ALA ASN SEQRES 2 A 118 ARG VAL PRO ALA GLY LEU GLU LYS ARG LEU CYS ALA ALA SEQRES 3 A 118 ALA ALA SER ILE LEU GLY LYS PRO ALA ASP ARG VAL ASN SEQRES 4 A 118 VAL THR VAL ARG PRO GLY LEU ALA MET ALA LEU SER GLY SEQRES 5 A 118 SER THR GLU PRO CYS ALA GLN LEU SER ILE SER SER ILE SEQRES 6 A 118 GLY VAL VAL GLY THR ALA GLU ASP ASN ARG SER HIS SER SEQRES 7 A 118 ALA HIS PHE PHE GLU PHE LEU THR LYS GLU LEU ALA LEU SEQRES 8 A 118 GLY GLN ASP ARG ILE LEU ILE ARG PHE PHE PRO LEU GLU SEQRES 9 A 118 SER TRP GLN ILE GLY LYS ILE GLY THR VAL MET THR PHE SEQRES 10 A 118 LEU HET SO4 A 201 5 HET NA A 202 1 HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION FORMUL 2 SO4 O4 S 2- FORMUL 3 NA NA 1+ FORMUL 4 HOH *76(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 ASP A 35 5 3 HELIX 4 AA4 THR A 69 ALA A 89 1 21 HELIX 5 AA5 GLY A 91 ASP A 93 5 3 HELIX 6 AA6 GLU A 103 GLN A 106 5 4 HELIX 7 AA7 THR A 115 LEU A 117 5 3 SHEET 1 AA1 4 VAL A 37 ARG A 42 0 SHEET 2 AA1 4 GLY A 1 THR A 7 1 N LEU A 5 O THR A 40 SHEET 3 AA1 4 ALA A 57 ILE A 64 -1 O SER A 62 N PHE A 2 SHEET 4 AA1 4 ILE A 95 LEU A 102 1 O ARG A 98 N ILE A 61 SHEET 1 AA2 2 GLY A 108 LYS A 109 0 SHEET 2 AA2 2 THR A 112 VAL A 113 -1 O THR A 112 N LYS A 109 LINK O4 SO4 A 201 NA NA A 202 1555 1555 2.72 LINK O2 SO4 A 201 NA NA A 202 1555 3455 3.16 LINK O3 SO4 A 201 NA NA A 202 1555 2565 3.17 LINK O4 SO4 A 201 NA NA A 202 1555 3455 2.71 LINK NA NA A 202 O HOH A 312 1555 1555 2.88 LINK NA NA A 202 O HOH A 321 1555 1555 2.69 LINK NA NA A 202 O HOH A 329 1555 2565 2.71 CRYST1 73.993 73.993 41.067 90.00 90.00 120.00 P 63 6 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 0.013515 0.007803 0.000000 0.00000 SCALE2 0.000000 0.015606 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024350 0.00000