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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
