HEADER TRANSCRIPTION 09-NOV-16 5H5P TITLE CRYSTAL STRUCTURE OF MYELIN-GENE REGULATORY FACTOR DNA BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELIN REGULATORY FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 351-532; COMPND 5 SYNONYM: MYELIN GENE REGULATORY FACTOR; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MYRF, GM1804, GM98, MRF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IG FOLD TRANSCRIPTION FACTOR, ER MEMBRANE PROTEIN, TRIMERIC KEYWDS 2 TRANSCRIPTION FACTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR N.SHI,X.ZHEN,B.LI REVDAT 2 18-OCT-17 5H5P 1 REMARK REVDAT 1 28-JUN-17 5H5P 0 JRNL AUTH X.ZHEN,B.LI,F.HU,S.YAN,G.MELONI,H.LI,N.SHI JRNL TITL CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF MYELIN-GENE JRNL TITL 2 REGULATORY FACTOR. JRNL REF SCI REP V. 7 3696 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28623291 JRNL DOI 10.1038/S41598-017-03768-9 REMARK 2 REMARK 2 RESOLUTION. 2.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 20442 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2038 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 34.0354 - 6.0578 1.00 1231 140 0.1711 0.2070 REMARK 3 2 6.0578 - 4.8126 1.00 1225 143 0.1501 0.1530 REMARK 3 3 4.8126 - 4.2055 1.00 1229 132 0.1295 0.1891 REMARK 3 4 4.2055 - 3.8216 1.00 1231 138 0.1449 0.1913 REMARK 3 5 3.8216 - 3.5480 1.00 1238 128 0.1620 0.2279 REMARK 3 6 3.5480 - 3.3390 1.00 1211 148 0.1675 0.2265 REMARK 3 7 3.3390 - 3.1719 1.00 1225 136 0.1830 0.2589 REMARK 3 8 3.1719 - 3.0339 1.00 1259 147 0.1969 0.2700 REMARK 3 9 3.0339 - 2.9172 1.00 1210 138 0.2065 0.2511 REMARK 3 10 2.9172 - 2.8166 1.00 1216 136 0.2302 0.2826 REMARK 3 11 2.8166 - 2.7285 1.00 1245 135 0.2188 0.2798 REMARK 3 12 2.7285 - 2.6506 1.00 1239 132 0.2356 0.3208 REMARK 3 13 2.6506 - 2.5808 1.00 1232 130 0.2212 0.2783 REMARK 3 14 2.5808 - 2.5179 1.00 1253 132 0.2589 0.3620 REMARK 3 15 2.5179 - 2.4606 0.95 1160 123 0.3909 0.4618 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 1536 REMARK 3 ANGLE : 1.209 2083 REMARK 3 CHIRALITY : 0.048 226 REMARK 3 PLANARITY : 0.005 272 REMARK 3 DIHEDRAL : 15.895 587 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 5H5P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1300002081. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24100 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.366 REMARK 200 RESOLUTION RANGE LOW (A) : 44.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, MAGNESIUM ACETATE, PEG4000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 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 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 51.98500 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -90.04066 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 103.97000 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 GLY A 347 REMARK 465 PRO A 348 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 ASP A 382 -77.84 -76.72 REMARK 500 LYS A 415 -29.03 -140.50 REMARK 500 ALA A 440 76.61 -155.26 REMARK 500 ARG A 454 18.34 59.67 REMARK 500 GLU A 469 18.25 57.24 REMARK 500 ASN A 487 35.61 70.77 REMARK 500 REMARK 500 REMARK: NULL DBREF 5H5P A 351 532 UNP Q3UR85 MRF_MOUSE 351 532 SEQADV 5H5P GLY A 347 UNP Q3UR85 EXPRESSION TAG SEQADV 5H5P PRO A 348 UNP Q3UR85 EXPRESSION TAG SEQADV 5H5P GLU A 349 UNP Q3UR85 EXPRESSION TAG SEQADV 5H5P ILE A 350 UNP Q3UR85 EXPRESSION TAG SEQRES 1 A 186 GLY PRO GLU ILE ILE LYS TRP GLN PRO HIS GLN GLN ASN SEQRES 2 A 186 LYS TRP ALA THR LEU TYR ASP ALA ASN TYR LYS GLU LEU SEQRES 3 A 186 PRO MSE LEU THR TYR ARG VAL ASP ALA ASP LYS GLY PHE SEQRES 4 A 186 ASN PHE SER VAL GLY ASP ASP ALA PHE VAL CYS GLN LYS SEQRES 5 A 186 LYS ASN HIS PHE GLN VAL THR VAL TYR ILE GLY MSE LEU SEQRES 6 A 186 GLY GLU PRO LYS TYR VAL LYS THR PRO GLU GLY LEU LYS SEQRES 7 A 186 PRO LEU ASP CYS PHE TYR LEU LYS LEU HIS GLY VAL LYS SEQRES 8 A 186 LEU GLU ALA LEU ASN GLN SER ILE ASN ILE GLU GLN SER SEQRES 9 A 186 GLN SER ASP ARG SER LYS ARG PRO PHE ASN PRO VAL THR SEQRES 10 A 186 VAL ASN LEU PRO PRO GLU GLN VAL THR LYS VAL THR VAL SEQRES 11 A 186 GLY ARG LEU HIS PHE SER GLU THR THR ALA ASN ASN MSE SEQRES 12 A 186 ARG LYS LYS GLY LYS PRO ASN PRO ASP GLN ARG TYR PHE SEQRES 13 A 186 MSE LEU VAL VAL ALA LEU GLN ALA HIS ALA GLN ASN GLN SEQRES 14 A 186 ASN TYR THR LEU ALA ALA GLN ILE SER GLU ARG ILE ILE SEQRES 15 A 186 VAL ARG ALA SER MODRES 5H5P MSE A 374 MET MODIFIED RESIDUE MODRES 5H5P MSE A 410 MET MODIFIED RESIDUE MODRES 5H5P MSE A 489 MET MODIFIED RESIDUE MODRES 5H5P MSE A 503 MET MODIFIED RESIDUE HET MSE A 374 13 HET MSE A 410 8 HET MSE A 489 8 HET MSE A 503 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 HOH *21(H2 O) HELIX 1 AA1 GLN A 357 TRP A 361 5 5 SHEET 1 AA1 5 TRP A 353 PRO A 355 0 SHEET 2 AA1 5 GLN A 515 SER A 524 -1 O ILE A 523 N GLN A 354 SHEET 3 AA1 5 PHE A 502 ALA A 512 -1 N LEU A 508 O ALA A 520 SHEET 4 AA1 5 CYS A 428 LYS A 437 -1 N TYR A 430 O GLN A 509 SHEET 5 AA1 5 ALA A 440 ILE A 445 -1 O ILE A 445 N GLY A 435 SHEET 1 AA2 5 TRP A 353 PRO A 355 0 SHEET 2 AA2 5 GLN A 515 SER A 524 -1 O ILE A 523 N GLN A 354 SHEET 3 AA2 5 PHE A 502 ALA A 512 -1 N LEU A 508 O ALA A 520 SHEET 4 AA2 5 CYS A 428 LYS A 437 -1 N TYR A 430 O GLN A 509 SHEET 5 AA2 5 VAL A 462 VAL A 464 -1 O VAL A 462 N LEU A 431 SHEET 1 AA3 3 THR A 363 ASP A 366 0 SHEET 2 AA3 3 PRO A 414 THR A 419 -1 O TYR A 416 N TYR A 365 SHEET 3 AA3 3 GLY A 422 PRO A 425 -1 O LYS A 424 N VAL A 417 SHEET 1 AA4 5 THR A 376 ASP A 380 0 SHEET 2 AA4 5 PHE A 402 GLY A 409 -1 O THR A 405 N ASP A 380 SHEET 3 AA4 5 VAL A 471 PHE A 481 -1 O VAL A 476 N VAL A 404 SHEET 4 AA4 5 ILE A 447 SER A 450 -1 N GLU A 448 O HIS A 480 SHEET 5 AA4 5 LYS A 456 PRO A 458 -1 O ARG A 457 N GLN A 449 SHEET 1 AA5 3 ASN A 386 SER A 388 0 SHEET 2 AA5 3 ALA A 393 GLN A 397 -1 O VAL A 395 N ASN A 386 SHEET 3 AA5 3 ILE A 527 ARG A 530 1 O ILE A 528 N PHE A 394 LINK C PRO A 373 N MSE A 374 1555 1555 1.33 LINK C MSE A 374 N LEU A 375 1555 1555 1.32 LINK C GLY A 409 N MSE A 410 1555 1555 1.33 LINK C MSE A 410 N LEU A 411 1555 1555 1.33 LINK C ASN A 488 N MSE A 489 1555 1555 1.33 LINK C MSE A 489 N ARG A 490 1555 1555 1.33 LINK C PHE A 502 N MSE A 503 1555 1555 1.32 LINK C MSE A 503 N LEU A 504 1555 1555 1.33 CRYST1 103.970 103.970 46.730 90.00 90.00 120.00 P 3 2 1 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 0.009618 0.005553 0.000000 0.00000 SCALE2 0.000000 0.011106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021400 0.00000