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- PDB-8x33: crystal structure of the CobH-like domain in cobalt regulator CoaR -

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Basic information

Entry
Database: PDB / ID: 8x33
Titlecrystal structure of the CobH-like domain in cobalt regulator CoaR
ComponentsMercuric resistance operon regulatory protein precorrin isomerase
KeywordsMETAL BINDING PROTEIN / cobalt binding / corrin binding
Function / homology
Function and homology information


precorrin-8X methylmutase activity / cobalamin biosynthetic process / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Cobalamin biosynthesis precorrin-8X methylmutase CobH/CbiC / Precorrin-8X methylmutase CobH/CbiC superfamily / Precorrin-8X methylmutase / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
Mercuric resistance operon regulatory protein precorrin isomerase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLiu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)22107046 China
CitationJournal: To Be Published
Title: crystal structure of the CobH-like domain in cobalt regulator CoaR
Authors: Xichun, L.
History
DepositionNov 10, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mercuric resistance operon regulatory protein precorrin isomerase
B: Mercuric resistance operon regulatory protein precorrin isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8928
Polymers46,6802
Non-polymers2136
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, CobH-like domain
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-50 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.236, 96.236, 148.889
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 165 - 358 / Label seq-ID: 14 - 207

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.190203263466, -0.981734382593, 0.00450783790258), (-0.981727498279, -0.190225126017, -0.0050517871853), (0.00581701720644, -0.00346460201777, -0.999977079159)Vector: - ...NCS oper: (Code: given
Matrix: (0.190203263466, -0.981734382593, 0.00450783790258), (-0.981727498279, -0.190225126017, -0.0050517871853), (0.00581701720644, -0.00346460201777, -0.999977079159)
Vector: -0.0305096345329, -0.270135128488, -48.99410053)

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Components

#1: Protein Mercuric resistance operon regulatory protein precorrin isomerase


Mass: 23339.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: merR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q55938
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestN
Has protein modificationN

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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: 4.26 Å3/Da / Density % sol: 71.15 % / Description: hexagonal prism shape
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Bis-Tris, (NH4)2SO4, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→83.34 Å / Num. obs: 12954 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.402 / Rpim(I) all: 0.149 / Rrim(I) all: 0.43 / Net I/σ(I): 5.2
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 8.3 % / Rmerge(I) obs: 2.35 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1856 / Rpim(I) all: 0.875 / Rrim(I) all: 2.51 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.12 Å / SU ML: 0.3797 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.2084
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2342 636 4.95 %
Rwork0.1855 12200 -
obs0.1879 12836 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.75 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 6 0 2904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01162956
X-RAY DIFFRACTIONf_angle_d1.34854042
X-RAY DIFFRACTIONf_chiral_restr0.0669500
X-RAY DIFFRACTIONf_plane_restr0.0119516
X-RAY DIFFRACTIONf_dihedral_angle_d6.6634404
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.480283011717 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.30541200.26822384X-RAY DIFFRACTION97.62
3.45-3.790.25411350.22012422X-RAY DIFFRACTION99.65
3.79-4.340.23551260.17622469X-RAY DIFFRACTION100
4.34-5.470.19191300.15912442X-RAY DIFFRACTION99.96
5.47-48.120.22521250.16192483X-RAY DIFFRACTION99.73

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