HEADER OXIDOREDUCTASE 29-JUN-16 5LE0 TITLE MICAL1 CTERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-METHIONINE SULFOXIDE OXIDASE MICAL1; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: UNP RESIDUES 918-1067; COMPND 5 SYNONYM: MOLECULE INTERACTING WITH CASL PROTEIN 1,MICAL-1,NEDD9- COMPND 6 INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS; COMPND 7 EC: 1.14.13.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MICAL1, MICAL, NICAL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MICAL, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.HAMMICH,O.PYLYPENKO,A.HOUDUSSE REVDAT 2 08-MAR-17 5LE0 1 JRNL REVDAT 1 01-MAR-17 5LE0 0 JRNL AUTH S.FREMONT,H.HAMMICH,J.BAI,H.WIOLAND,K.KLINKERT,M.ROCANCOURT, JRNL AUTH 2 C.KIKUTI,D.STROEBEL,G.ROMET-LEMONNE,O.PYLYPENKO,A.HOUDUSSE, JRNL AUTH 3 A.ECHARD JRNL TITL OXIDATION OF F-ACTIN CONTROLS THE TERMINAL STEPS OF JRNL TITL 2 CYTOKINESIS. JRNL REF NAT COMMUN V. 8 14528 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 28230050 JRNL DOI 10.1038/NCOMMS14528 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 3729 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.273 REMARK 3 R VALUE (WORKING SET) : 0.271 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 185 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 3.4179 - 3.3000 0.99 338 18 0.3117 0.4159 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.230 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 : 0.005 958 REMARK 3 ANGLE : 0.597 1287 REMARK 3 CHIRALITY : 0.031 153 REMARK 3 PLANARITY : 0.003 171 REMARK 3 DIHEDRAL : 9.982 605 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 5LE0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000597. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-15 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978870 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3734 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 43.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31700 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 (%): 67.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: EG, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.50000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 117.75000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.25000 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 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 78.50000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.25000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 117.75000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 LYS B 918 REMARK 465 GLU B 919 REMARK 465 GLU B 920 REMARK 465 GLU B 921 REMARK 465 MSE B 922 REMARK 465 LYS B 923 REMARK 465 ARG B 924 REMARK 465 ALA B 955 REMARK 465 LEU B 956 REMARK 465 ARG B 957 REMARK 465 ARG B 958 REMARK 465 GLN B 959 REMARK 465 SER B 960 REMARK 465 SER B 961 REMARK 465 SER B 962 REMARK 465 PRO B 963 REMARK 465 ARG B 1017 REMARK 465 GLU B 1018 REMARK 465 GLU B 1019 REMARK 465 ALA B 1060 REMARK 465 LEU B 1061 REMARK 465 GLY B 1062 REMARK 465 THR B 1063 REMARK 465 GLY B 1064 REMARK 465 ALA B 1065 REMARK 465 GLN B 1066 REMARK 465 GLY B 1067 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 CYS B 926 SG REMARK 470 GLN B 929 CG CD OE1 NE2 REMARK 470 LYS B 951 CG CD CE NZ REMARK 470 LEU B 954 CG CD1 CD2 REMARK 470 GLU B 964 CG CD OE1 OE2 REMARK 470 GLN B 965 CG CD OE1 NE2 REMARK 470 GLN B 966 CG CD OE1 NE2 REMARK 470 LYS B 967 CG CD CE NZ REMARK 470 LYS B 968 CG CD CE NZ REMARK 470 TRP B 970 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 970 CZ3 CH2 REMARK 470 ASN B1016 CG OD1 ND2 REMARK 470 ASN B1020 CG OD1 ND2 REMARK 470 LEU B1021 CG CD1 CD2 REMARK 470 LYS B1022 CG CD CE NZ REMARK 470 THR B1023 OG1 CG2 REMARK 470 ASP B1026 CG OD1 OD2 REMARK 470 LEU B1037 CG CD1 CD2 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 OD1 ASN B 936 HD22 ASN B 1042 7555 1.51 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 ALA B 928 30.18 -86.38 REMARK 500 LYS B1003 20.23 -73.88 REMARK 500 REMARK 500 REMARK: NULL DBREF 5LE0 B 918 1067 UNP Q8TDZ2 MICA1_HUMAN 918 1067 SEQRES 1 B 150 LYS GLU GLU GLU MSE LYS ARG PHE CYS LYS ALA GLN THR SEQRES 2 B 150 ILE GLN ARG ARG LEU ASN GLU ILE GLU ALA ALA LEU ARG SEQRES 3 B 150 GLU LEU GLU ALA GLU GLY VAL LYS LEU GLU LEU ALA LEU SEQRES 4 B 150 ARG ARG GLN SER SER SER PRO GLU GLN GLN LYS LYS LEU SEQRES 5 B 150 TRP VAL GLY GLN LEU LEU GLN LEU VAL ASP LYS LYS ASN SEQRES 6 B 150 SER LEU VAL ALA GLU GLU ALA GLU LEU MSE ILE THR VAL SEQRES 7 B 150 GLN GLU LEU ASN LEU GLU GLU LYS GLN TRP GLN LEU ASP SEQRES 8 B 150 GLN GLU LEU ARG GLY TYR MSE ASN ARG GLU GLU ASN LEU SEQRES 9 B 150 LYS THR ALA ALA ASP ARG GLN ALA GLU ASP GLN VAL LEU SEQRES 10 B 150 ARG LYS LEU VAL ASP LEU VAL ASN GLN ARG ASP ALA LEU SEQRES 11 B 150 ILE ARG PHE GLN GLU GLU ARG ARG LEU SER GLU LEU ALA SEQRES 12 B 150 LEU GLY THR GLY ALA GLN GLY MODRES 5LE0 MSE B 992 MET MODIFIED RESIDUE MODRES 5LE0 MSE B 1015 MET MODIFIED RESIDUE HET MSE B 992 17 HET MSE B1015 17 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) HELIX 1 AA1 GLN B 929 LEU B 954 1 26 HELIX 2 AA2 GLN B 965 ASN B 1016 1 52 HELIX 3 AA3 THR B 1023 GLU B 1058 1 36 LINK C LEU B 991 N MSE B 992 1555 1555 1.33 LINK C MSE B 992 N ILE B 993 1555 1555 1.33 LINK C TYR B1014 N MSE B1015 1555 1555 1.33 LINK C MSE B1015 N ASN B1016 1555 1555 1.33 CRYST1 52.780 52.780 157.000 90.00 90.00 90.00 P 43 2 2 8 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 0.018947 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018947 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006369 0.00000