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- PDB-9ika: Crystal structure of the tetrapyrrole binding domain in CoaR -

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Basic information

Entry
Database: PDB / ID: 9ika
TitleCrystal structure of the tetrapyrrole binding domain in CoaR
ComponentsMercuric resistance operon regulatory protein precorrin isomerase
KeywordsMETAL BINDING PROTEIN / corrin binding / cobalt response
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
DI(HYDROXYETHYL)ETHER / Mercuric resistance operon regulatory protein precorrin isomerase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsLiu, X.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Crystal structure of the tetrapyrrole binding domain in CoaR
Authors: Liu, X.C.
History
DepositionJun 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 2, 2025Provider: 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)46,7024
Polymers46,5032
Non-polymers1982
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-11 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.365, 101.500, 48.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Mercuric resistance operon regulatory protein precorrin isomerase


Mass: 23251.732 Da / Num. of mol.: 2 / Fragment: tetrapyrrole binding domain
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: (NH4)2SO4, Tris, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97881 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97881 Å / Relative weight: 1
ReflectionResolution: 2.26→34.58 Å / Num. obs: 22245 / % possible obs: 98.4 % / Redundancy: 9.6 % / Biso Wilson estimate: 29.59 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.035 / Rrim(I) all: 0.11 / Net I/σ(I): 15.9
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1421 / CC1/2: 0.22 / Rpim(I) all: 0.533 / Rrim(I) all: 0.997 / % possible all: 87.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→34.56 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.56 / SU ML: 0.133 / Cross valid method: FREE R-VALUE / ESU R: 0.233 / ESU R Free: 0.175
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2097 1076 4.848 %
Rwork0.1921 21121 -
all0.193 --
obs-22197 98.009 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.602 Å2
Baniso -1Baniso -2Baniso -3
1-1.195 Å2-0 Å20 Å2
2---2.278 Å20 Å2
3---1.084 Å2
Refinement stepCycle: LAST / Resolution: 2.26→34.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 12 119 2770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122693
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162713
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.7963672
X-RAY DIFFRACTIONr_angle_other_deg0.3961.7246234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8685354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.946512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58210443
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.5221089
X-RAY DIFFRACTIONr_chiral_restr0.0530.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02523
X-RAY DIFFRACTIONr_nbd_refined0.1870.2530
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22171
X-RAY DIFFRACTIONr_nbtor_refined0.1570.21282
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21360
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.280
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1310.28
X-RAY DIFFRACTIONr_nbd_other0.20.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.110.29
X-RAY DIFFRACTIONr_mcbond_it1.8823.4721428
X-RAY DIFFRACTIONr_mcbond_other1.8813.4721428
X-RAY DIFFRACTIONr_mcangle_it3.2046.2281778
X-RAY DIFFRACTIONr_mcangle_other3.2036.2311779
X-RAY DIFFRACTIONr_scbond_it2.3363.9071265
X-RAY DIFFRACTIONr_scbond_other2.3363.9091266
X-RAY DIFFRACTIONr_scangle_it4.1247.0071894
X-RAY DIFFRACTIONr_scangle_other4.1237.0081895
X-RAY DIFFRACTIONr_lrange_it6.1533.7632817
X-RAY DIFFRACTIONr_lrange_other6.07733.2112800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.3160.292590.2971325X-RAY DIFFRACTION83.7266
2.316-2.380.28870.2631389X-RAY DIFFRACTION94.0727
2.38-2.4480.279690.2211439X-RAY DIFFRACTION96.1122
2.448-2.5230.268770.2211419X-RAY DIFFRACTION99.4681
2.523-2.6050.214850.2241389X-RAY DIFFRACTION100
2.605-2.6960.22780.2151336X-RAY DIFFRACTION99.8588
2.696-2.7970.246740.2051287X-RAY DIFFRACTION99.9266
2.797-2.9110.294500.1941272X-RAY DIFFRACTION99.8489
2.911-3.0390.241580.2041239X-RAY DIFFRACTION99.846
3.039-3.1860.254530.1941156X-RAY DIFFRACTION100
3.186-3.3570.237620.1981092X-RAY DIFFRACTION99.9134
3.357-3.5590.167390.1891075X-RAY DIFFRACTION99.8208
3.559-3.8020.221390.1911012X-RAY DIFFRACTION100
3.802-4.1020.192450.165935X-RAY DIFFRACTION100
4.102-4.4870.179300.165876X-RAY DIFFRACTION100
4.487-5.0060.128400.146778X-RAY DIFFRACTION100
5.006-5.7610.219420.166701X-RAY DIFFRACTION100
5.761-7.0070.189320.208618X-RAY DIFFRACTION100
7.007-9.7120.146430.152470X-RAY DIFFRACTION100
9.712-34.5560.184140.204313X-RAY DIFFRACTION100

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