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- PDB-9ikt: Crystal structure of the tetrapyrrole binding domain in CoaR at 2... -

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Basic information

Entry
Database: PDB / ID: 9ikt
TitleCrystal structure of the tetrapyrrole binding domain in CoaR at 2 angstrom resolution
ComponentsMercuric resistance operon regulatory protein precorrin isomerase
KeywordsMETAL BINDING PROTEIN / CoaR / tetrapyrrole binding / cobalt 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
DI(HYDROXYETHYL)ETHER / Mercuric resistance operon regulatory protein precorrin isomerase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 at 2 angstrom resolution
Authors: Liu, X.C.
History
DepositionJun 28, 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

Downloads & links

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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)46,8866
Polymers46,5032
Non-polymers3824
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-16 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.854, 100.465, 48.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: BICINE, PEG 3350

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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: 2.03→34.1 Å / Num. obs: 29854 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 29.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.037 / Rrim(I) all: 0.128 / Net I/σ(I): 15.1
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2167 / CC1/2: 0.808 / Rpim(I) all: 0.546 / Rrim(I) all: 1.638 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→34.09 Å / SU ML: 0.2093 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0976
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 1456 4.91 %RANDOM
Rwork0.1912 28221 --
obs0.1926 29677 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.58 Å2
Refinement stepCycle: LAST / Resolution: 2.03→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 25 111 2809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672755
X-RAY DIFFRACTIONf_angle_d0.85413760
X-RAY DIFFRACTIONf_chiral_restr0.0541471
X-RAY DIFFRACTIONf_plane_restr0.0072475
X-RAY DIFFRACTIONf_dihedral_angle_d6.0699388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.10.38111450.32182718X-RAY DIFFRACTION97.68
2.1-2.190.28821460.24622788X-RAY DIFFRACTION99.69
2.19-2.290.29271550.25772745X-RAY DIFFRACTION98.77
2.29-2.410.22991440.19882785X-RAY DIFFRACTION99.8
2.41-2.560.24841400.20192779X-RAY DIFFRACTION99.73
2.56-2.750.2371410.21052813X-RAY DIFFRACTION99.83
2.75-3.030.2221390.20222847X-RAY DIFFRACTION99.9
3.03-3.470.23971470.18742854X-RAY DIFFRACTION99.93
3.47-4.370.18391330.16332892X-RAY DIFFRACTION99.97
4.37-34.090.17671660.16013000X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.26557043485-0.34836298107-0.05747673448511.927330920060.0111828324891.119538180130.1286438075230.1150567471650.398876006734-0.036992575046-0.107153238088-0.245013573652-0.05832006478710.0919202174243-0.01061444586610.3198703997270.0119319832820.06673345156150.2543813368270.05578057457750.36667113018137.82974612977.614166408410.6684952984
21.61000470045-0.128029890362-0.4515788522822.82218588652-0.2869514650722.42623289454-0.101768348130.3462491524880.00285945456748-0.4903577457920.3409627670140.01132614427990.0745310229373-0.206950388373-0.1046992032520.292204850311-0.07003314528260.00300955849190.270770401911-0.01297898444460.27471485417927.3262980283-10.51985990629.14918055052
34.94950206413-0.593015571233-2.17625394623.128226681051.549493010144.489555613110.108790041183-0.410774420447-0.363922362920.03750303742180.3365986526250.9284718591040.394658269826-0.793548372201-0.1178207053110.235319409537-0.0570694278008-0.001256010567320.3934330270650.1539966752040.4824492434518.7960313544-17.116304243226.3506428759
41.32222924017-0.2293225386720.2372338910842.73248900486-1.618032334292.40798610470.0149470007928-0.08057197739410.05097261470950.1552195437850.0942725398368-0.160238897529-0.2409757293050.0222664310449-0.06165092927670.241717220373-0.01511899736750.03851052173290.203384311111-0.003485226892030.281198003631.9259691986-8.2410567201620.9693607847
53.37535714445-2.002551404580.3838944032452.8530822991.038807702511.43829000872-0.499346031364-0.748777237862-0.294200011811.268858369220.3158940120970.2442508038830.0120722359278-0.531536637878-0.05862565319860.6251289124710.1755740618490.1794197867180.5139184762090.04582051831320.42515435562415.41402742037.0467577555131.9668837024
60.761332366721-0.9950367857940.1419293641153.26467202743-0.9844309819911.52211743658-0.156755330311-0.151825378708-0.04529335742320.6582769958370.281040156560.003835452810670.08826018648080.00369127402827-0.01382209693790.3713433150080.023778130390.07045051176580.270730532480.03556894212590.34444907893117.235983421810.857018683423.0700770581
72.503083641530.8247610073671.22016096652.561385912130.09663283785985.34709129861-0.0136152501283-0.2937457781870.0101917169622-0.02503819425910.07484414284640.912727997587-0.116016103269-0.9847026298630.1210588437290.204562799306-0.0701697594115-0.003614010062430.3818944573470.02315092300340.5240192416044.1283821256316.462569613313.7910365309
82.27762839992-1.189484966740.6730618713062.508130909990.1903824928691.933533958020.160118766222-0.0158121863266-0.554778329633-0.54627480891-0.1953696897440.3652533556930.618306516731-0.408213408157-0.05761499362410.484996450767-0.0943468620752-0.02959436548940.29958335808-0.07517997748790.44196864622712.1835616538.046836040273.29776544866
91.835803333472.47873075533-1.858233533614.07362025734-3.145886375542.44229185457-0.1873320520611.42644068562-0.334557012832-1.69080966491-0.127277004442-0.3738023616780.5882474062220.693306084829-0.09249712305420.9205346968970.04508860630050.1390283325560.633013316154-0.05224609940110.41745121356322.804083339818.0488521592-8.22159679767
102.63822453906-0.601499416805-0.02020884184563.01380910163-0.5025262246162.78270018260.0636030559960.4264788379070.197640439822-1.04927144664-0.01914847691390.067833350357-0.145105544914-0.320978560635-0.008310051042280.555298101345-0.00447372053581-0.05941494784960.327702233213-0.007035999942370.34512697506914.484541900921.9482868143-3.00429094935
112.04287908459-0.9890511010550.4536163225642.85329536457-0.621084565362.57633106468-0.001940723704790.04163920498490.186254266328-0.321358841928-0.0449357506515-0.232760234011-0.0592915913773-0.05938494226910.06673862276930.287704281049-0.01051797179590.04898845960180.1942418385240.005199370849020.24088712249118.739135097223.34909416186.35150847863
126.76081441967-0.314681363837-1.259444166983.368719777411.428384293582.33679853947-0.260011775632-0.1031814706530.345734208774-0.0331700905290.219124030839-0.0249841936073-0.2255627380290.1520267169140.1143696199650.216871095812-0.01775655863370.04831616046650.206026916325-0.02887216214160.28413941305422.352364304526.799371540813.8072555779
131.48711180431-1.646140833590.09002253306114.38576203662-0.5879132409822.645361538860.0222309857702-0.039215049782-0.204142201579-0.03754465449270.0303149236064-0.1941060015690.360444336585-0.0824251046214-0.009490535788770.227009419058-0.03481875002270.01680826933670.1938863180450.015581870790.29399572065315.059926342214.460050673514.5072334607
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 165 through 204 )AA165 - 2041 - 40
22chain 'A' and (resid 205 through 247 )AA205 - 24741 - 83
33chain 'A' and (resid 248 through 276 )AA248 - 27684 - 102
44chain 'A' and (resid 277 through 358 )AA277 - 358103 - 184
55chain 'B' and (resid 165 through 179 )BD165 - 1791 - 15
66chain 'B' and (resid 180 through 204 )BD180 - 20416 - 40
77chain 'B' and (resid 205 through 217 )BD205 - 21741 - 53
88chain 'B' and (resid 218 through 247 )BD218 - 24754 - 83
99chain 'B' and (resid 248 through 269 )BD248 - 26984 - 91
1010chain 'B' and (resid 270 through 281 )BD270 - 28192 - 103
1111chain 'B' and (resid 282 through 318 )BD282 - 318104 - 140
1212chain 'B' and (resid 319 through 327 )BD319 - 327141 - 149
1313chain 'B' and (resid 328 through 358 )BD328 - 358150 - 180

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