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- PDB-6nte: Crystal Structure of Synechocystis Dihydroxyacid Dehydratase (DHAD) -

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Basic information

Entry
Database: PDB / ID: 6nte
TitleCrystal Structure of Synechocystis Dihydroxyacid Dehydratase (DHAD)
ComponentsDihydroxy-acid dehydratase
KeywordsLYASE / Dehydratase
Function / homology
Function and homology information


dihydroxy-acid dehydratase / dihydroxy-acid dehydratase activity / branched-chain amino acid biosynthetic process / hydro-lyase activity / valine biosynthetic process / isoleucine biosynthetic process / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Dihydroxy-acid dehydratase / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 2. / Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 1. / Dihydroxy-acid/6-phosphogluconate dehydratase / IlvD/EDD, N-terminal domain / Dihydroxy-acid dehydratase, C-terminal / Dehydratase family
Similarity search - Domain/homology
Dihydroxy-acid dehydratase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsMacTavish, B. / Bruner, S.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Cyanobacterial Dihydroxyacid Dehydratases Are a Promising Growth Inhibition Target.
Authors: Zhang, P. / MacTavish, B.S. / Yang, G. / Chen, M. / Roh, J. / Newsome, K.R. / Bruner, S.D. / Ding, Y.
History
DepositionJan 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroxy-acid dehydratase
B: Dihydroxy-acid dehydratase


Theoretical massNumber of molelcules
Total (without water)117,3962
Polymers117,3962
Non-polymers00
Water4,612256
1
A: Dihydroxy-acid dehydratase


Theoretical massNumber of molelcules
Total (without water)58,6981
Polymers58,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydroxy-acid dehydratase


Theoretical massNumber of molelcules
Total (without water)58,6981
Polymers58,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.790, 74.258, 80.680
Angle α, β, γ (deg.)90.000, 90.148, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSILEILE(chain 'A' and (resid 35 through 150 or resid 193 through 561))AA35 - 14935 - 149
12GLYGLYLEULEU(chain 'A' and (resid 35 through 150 or resid 193 through 561))AA193 - 560193 - 560
21LYSLYSILEILEchain 'B'BB35 - 14935 - 149
22GLYGLYLEULEUchain 'B'BB193 - 560193 - 560

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Components

#1: Protein Dihydroxy-acid dehydratase / DAD


Mass: 58697.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Gene: ilvD, slr0452 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P74689, dihydroxy-acid dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.04 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M BIS-TRIS, 25% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.33→37.13 Å / Num. obs: 40235 / % possible obs: 99.15 % / Redundancy: 4.7 % / Biso Wilson estimate: 30.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1105 / Rpim(I) all: 0.05597 / Rrim(I) all: 0.1243 / Net I/σ(I): 12.12
Reflection shellResolution: 2.33→2.413 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.7135 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 3829 / CC1/2: 0.709 / Rpim(I) all: 0.3678 / Rrim(I) all: 0.8051 / % possible all: 95.25

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gp4

2gp4


Resolution: 2.33→37.13 Å / SU ML: 0.2632 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.6086
RfactorNum. reflection% reflection
Rfree0.2249 2153 5.35 %
Rwork0.1724 --
obs0.1752 40228 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.9 Å2
Refinement stepCycle: LAST / Resolution: 2.33→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7023 0 0 256 7279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00847132
X-RAY DIFFRACTIONf_angle_d0.98849678
X-RAY DIFFRACTIONf_chiral_restr0.05431149
X-RAY DIFFRACTIONf_plane_restr0.00641260
X-RAY DIFFRACTIONf_dihedral_angle_d8.89454314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.380.30781340.23952336X-RAY DIFFRACTION91.69
2.38-2.440.28621540.20462511X-RAY DIFFRACTION100
2.44-2.510.27441470.20142527X-RAY DIFFRACTION99.93
2.51-2.580.27651380.20092565X-RAY DIFFRACTION99.93
2.58-2.670.2729990.1982587X-RAY DIFFRACTION99.89
2.67-2.760.25421320.19112529X-RAY DIFFRACTION99.81
2.76-2.870.26651600.18192545X-RAY DIFFRACTION99.96
2.87-30.22751750.17442495X-RAY DIFFRACTION99.96
3-3.160.25991460.17742550X-RAY DIFFRACTION99.89
3.16-3.360.21161200.16882573X-RAY DIFFRACTION99.85
3.36-3.620.21511300.15742563X-RAY DIFFRACTION99.63
3.62-3.980.20981460.15882547X-RAY DIFFRACTION99.37
3.98-4.560.19481670.14352548X-RAY DIFFRACTION99.74
4.56-5.740.19671520.16642575X-RAY DIFFRACTION99.89
5.74-37.130.19281530.16972624X-RAY DIFFRACTION99.64

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