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- PDB-6is8: Crystal structure of ZmMoc1 D115N mutant in complex with Holliday... -

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Basic information

Entry
Database: PDB / ID: 6is8
TitleCrystal structure of ZmMoc1 D115N mutant in complex with Holliday junction
Components
  • (DNA (33-MER)) x 2
  • Monokaryotic chloroplast 1
KeywordsDNA BINDING PROTEIN/DNA / Holliday junction resolvase-DNA complex / DNA BINDING PROTEIN-DNA complex
Function / homologyHolliday junction resolvase MOC1-like / crossover junction DNA endonuclease activity / DNA / DNA (> 10) / Holliday junction resolvase MOC1, chloroplastic
Function and homology information
Biological speciesZea mays (maize)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsLin, Z. / Lin, H. / Zhang, D. / Yuan, C.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Structural basis of sequence-specific Holliday junction cleavage by MOC1.
Authors: Lin, H. / Zhang, D. / Zuo, K. / Yuan, C. / Li, J. / Huang, M. / Lin, Z.
History
DepositionNov 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.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.pdbx_ptnr1_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monokaryotic chloroplast 1
B: Monokaryotic chloroplast 1
C: DNA (33-MER)
D: DNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2228
Polymers57,6974
Non-polymers5254
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11730 Å2
ΔGint-97 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.699, 77.907, 63.577
Angle α, β, γ (deg.)90.00, 97.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Monokaryotic chloroplast 1


Mass: 18711.361 Da / Num. of mol.: 2 / Fragment: RuvC domain / Mutation: D115N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4FCI7

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (33-MER)


Mass: 10121.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (33-MER)


Mass: 10152.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 482 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.21 % / Mosaicity: 0.421 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5 / Details: 0.1 M Bis-tris pH 7.5, 37.5% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 58742 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.024 / Rrim(I) all: 0.062 / Χ2: 0.973 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.68-1.746.70.76558270.8110.3170.8290.88599.5
1.74-1.816.40.55958500.8760.2370.6080.91499.3
1.81-1.896.80.37958530.9410.1560.4110.97499.7
1.89-1.996.90.23258550.9770.0940.2510.9599.6
1.99-2.126.70.15658570.9870.0640.1690.97899.6
2.12-2.286.60.11158410.9930.0460.121.01999.3
2.28-2.5170.07959100.9960.0320.0850.97599.8
2.51-2.876.60.06158770.9970.0250.0660.97699.3
2.87-3.627.10.05158960.9980.0210.0551.02299.7
3.62-506.60.04559760.9970.0190.0481.03199.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IS9

6is9


Resolution: 1.68→49 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 2756 4.9 %
Rwork0.1572 --
obs0.1595 56212 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 1324 34 478 4320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074141
X-RAY DIFFRACTIONf_angle_d0.7965902
X-RAY DIFFRACTIONf_dihedral_angle_d15.8672762
X-RAY DIFFRACTIONf_chiral_restr0.052654
X-RAY DIFFRACTIONf_plane_restr0.006528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6804-1.70940.319930.22551583X-RAY DIFFRACTION58
1.7094-1.74050.28791130.20672053X-RAY DIFFRACTION73
1.7405-1.7740.26661390.19942430X-RAY DIFFRACTION87
1.774-1.81020.23491260.18442609X-RAY DIFFRACTION93
1.8102-1.84950.24721400.17622743X-RAY DIFFRACTION98
1.8495-1.89260.23581370.16482806X-RAY DIFFRACTION100
1.8926-1.93990.22151350.15482767X-RAY DIFFRACTION100
1.9399-1.99240.19421500.14722802X-RAY DIFFRACTION100
1.9924-2.0510.21391440.15032799X-RAY DIFFRACTION100
2.051-2.11720.20121540.15172752X-RAY DIFFRACTION100
2.1172-2.19290.17741420.14842776X-RAY DIFFRACTION99
2.1929-2.28070.20021290.14642813X-RAY DIFFRACTION100
2.2807-2.38440.19251450.14392806X-RAY DIFFRACTION100
2.3844-2.51020.1831250.14632835X-RAY DIFFRACTION100
2.5102-2.66740.20091540.1512786X-RAY DIFFRACTION100
2.6674-2.87330.22081360.17112820X-RAY DIFFRACTION99
2.8733-3.16250.1821560.16512789X-RAY DIFFRACTION100
3.1625-3.61990.23811430.15212811X-RAY DIFFRACTION100
3.6199-4.56020.16631470.13862824X-RAY DIFFRACTION99
4.5602-49.02040.18481480.16462852X-RAY DIFFRACTION99

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