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- PDB-4v82: Crystal structure of cyanobacterial Photosystem II in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4v82
TitleCrystal structure of cyanobacterial Photosystem II in complex with terbutryn
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 16
  • Cytochrome c-550
  • Photosystem Q(B) protein 1
KeywordsPHOTOSYNTHESIS / TRANSMEMBRANE ALPHA-HELIX / PS II / PS2 / ELECTRON TRANSPORT PHOTOSYSTEM / HERBICIDE RESISTANCE / PHOTOSYSTEM II / REACTION CENTER / IRON / METAL-BINDING / HEME / MANGANESE / MEMBRANE COMPLEX / THYLAKOID
Function / homology
Function and homology information


photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide / extrinsic component of membrane / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / phosphate ion binding / : / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbX, type 1 subfamily ...Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-MST / OXYGEN EVOLVING SYSTEM ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-MST / OXYGEN EVOLVING SYSTEM / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Photosystem II extrinsic protein V / Photosystem II extrinsic protein O / Photosystem II protein D1 1 / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein K / Photosystem II extrinsic protein U / Photosystem II reaction center protein X
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGabdulkhakov, A. / Broser, M. / Guskov, A. / Kern, J. / Glockner, C. / Muh, F. / Saenger, W. / Zouni, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural basis of cyanobacterial photosystem II Inhibition by the herbicide terbutryn
Authors: Broser, M. / Glockner, C. / Gabdulkhakov, A. / Guskov, A. / Buchta, J. / Kern, J. / Muh, F. / Dau, H. / Saenger, W. / Zouni, A.
History
DepositionNov 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3PRQ, 3PRR
Revision 1.1Dec 10, 2014Group: Other
Revision 2.0Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Photosystem Q(B) protein 1
AB: Photosystem II core light harvesting protein
AC: Photosystem II CP43 protein
AD: Photosystem II D2 protein
AE: Cytochrome b559 subunit alpha
AF: Cytochrome b559 subunit beta
AH: Photosystem II reaction center protein H
AI: Photosystem II reaction center protein I
AJ: Photosystem II reaction center protein J
AK: Photosystem II reaction center protein K
AL: Photosystem II reaction center protein L
AM: Photosystem II reaction center protein M
AO: Photosystem II manganese-stabilizing polypeptide
AT: Photosystem II reaction center protein T
AU: Photosystem II 12 kDa extrinsic protein
AV: Cytochrome c-550
Ay: Photosystem II reaction center protein ycf12
AX: Photosystem II reaction center X protein
AY: PHOTOSYSTEM II PSBX PROTEIN
AZ: Photosystem II reaction center protein Z
BA: Photosystem Q(B) protein 1
BB: Photosystem II core light harvesting protein
BC: Photosystem II CP43 protein
BD: Photosystem II D2 protein
BE: Cytochrome b559 subunit alpha
BF: Cytochrome b559 subunit beta
BH: Photosystem II reaction center protein H
BI: Photosystem II reaction center protein I
BJ: Photosystem II reaction center protein J
BK: Photosystem II reaction center protein K
BL: Photosystem II reaction center protein L
BM: Photosystem II reaction center protein M
BO: Photosystem II manganese-stabilizing polypeptide
BT: Photosystem II reaction center protein T
BU: Photosystem II 12 kDa extrinsic protein
BV: Cytochrome c-550
By: Photosystem II reaction center protein ycf12
BX: Photosystem II reaction center X protein
BY: PHOTOSYSTEM II PSBX PROTEIN
BZ: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)742,076234
Polymers607,27740
Non-polymers134,799194
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.080, 225.370, 305.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules AABAAVBV

#1: Protein Photosystem Q(B) protein 1 / 32 kDa thylakoid membrane protein 1 / Photosystem II protein D1 1


Mass: 38265.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A444
#16: Protein Cytochrome c-550 / Cytochrome c-549 / Cytochrome c550 / Low-potential cytochrome c


Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A386

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Photosystem II ... , 16 types, 32 molecules ABBBACBCADBDAHBHAIBIAJBJAKBKALBLAMBMAOBOATBTAUBUAyByAXBXAYBYAZBZ

#2: Protein Photosystem II core light harvesting protein


Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ1
#3: Protein Photosystem II CP43 protein


Mass: 50287.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIF8
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8CM25
#7: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJ43
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJZ6
#9: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P59087
#10: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1K9
#11: Protein/peptide Photosystem II reaction center protein L / PSII-L / PSII 5 kDa protein


Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIN8
#12: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHA7
#13: Protein Photosystem II manganese-stabilizing polypeptide / MSP


Mass: 26923.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A431
#14: Protein/peptide Photosystem II reaction center protein T / PSII-T / PSII-Tc


Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ0
#15: Protein Photosystem II 12 kDa extrinsic protein / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 11655.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1L5
#17: Protein/peptide Photosystem II reaction center protein ycf12


Mass: 5039.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJI1
#18: Protein/peptide Photosystem II reaction center X protein


Mass: 4322.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1R6
#19: Protein/peptide PHOTOSYSTEM II PSBX PROTEIN


Mass: 2400.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) / Strain: BP-1
#20: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHJ2

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Cytochrome b559 subunit ... , 2 types, 4 molecules AEBEAFBF

#5: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIP0
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIN9

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Sugars , 2 types, 30 molecules

#28: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C51H96O15
#32: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 15 types, 164 molecules

#21: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#22: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#23: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#24: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#25: Chemical ChemComp-MST / 2-T-BUTYLAMINO-4-ETHYLAMINO-6-METHYLTHIO-S-TRIAZINE


Mass: 241.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H19N5S
#26: Chemical ChemComp-OEC / OXYGEN EVOLVING SYSTEM


Mass: 323.828 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O4
#27: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H56
#29: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#30: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C41H78O12S
#31: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C45H86O10
#33: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#34: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#35: Chemical ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#36: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#37: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

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Details

Has protein modificationY
Sequence detailsCHAIN Y:THE DEPOSITORS KNOW THE SEQUENCE. BUT THEY DON'T KNOW IF THE FIRST RESIDUE OF THE CHAIN IS ...CHAIN Y:THE DEPOSITORS KNOW THE SEQUENCE. BUT THEY DON'T KNOW IF THE FIRST RESIDUE OF THE CHAIN IS REALLY THE FIRST OF THE SEQUENCE. MET GLY MET ASP TRP ARG VAL LEU VAL VAL LEU LEU PRO VAL LEU LEU ALA ALA GLY TRP ALA VAL ARG ASN ILE LEU PRO TYR ALA VAL LYS GLN VAL GLN LYS LEU LEU GLN LYS ALA LYS ALA ALA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.14 %
Crystal growTemperature: 298 K / Method: batch / pH: 7
Details: Pipes, CaCl2, DMSO, PEG 2000, pH 7.0, batch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 137557 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.93 % / Biso Wilson estimate: 110 Å2 / Rmerge(I) obs: 0.158 / Rsym value: 0.129 / Net I/σ(I): 7.76
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 5.07 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.34 / Num. unique all: 12582 / Rsym value: 0.588 / % possible all: 90.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.3refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BZ1

3bz1
PDB Unreleased entry


Resolution: 3.2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 7881267.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.299 2751 2 %RANDOM
Rwork0.269 ---
all0.271 137557 --
obs0.269 136912 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.0364 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 120.3 Å2
Baniso -1Baniso -2Baniso -3
1-36.36 Å2-0 Å20 Å2
2---4.99 Å20 Å2
3----31.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.64 Å0.57 Å
Luzzati d res low-5 Å
Luzzati sigma a0.96 Å0.96 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20553 0 4579 0 25132
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_improper_angle_d1.41
X-RAY DIFFRACTIONc_mcbond_it0.971.5
X-RAY DIFFRACTIONc_mcangle_it1.722
X-RAY DIFFRACTIONc_scbond_it9.242
X-RAY DIFFRACTIONc_scangle_it10.62.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.486 429 2 %
Rwork0.462 20839 -
obs-21268 88.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6mst.paramcof-new6.top
X-RAY DIFFRACTION7cof-new6.parammst.top
X-RAY DIFFRACTION8dms.paramdms.top

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