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- PDB-6js9: Crystal structure of the N-terminal domain of HtaA from Corynebac... -

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Basic information

Entry
Database: PDB / ID: 6js9
TitleCrystal structure of the N-terminal domain of HtaA from Corynebacterium glutamicum
ComponentsHypothetical membrane protein
KeywordsHEME-BINDING PROTEIN / heme / heme transport
Function / homologyHtaa / Htaa / PROTOPORPHYRIN IX CONTAINING FE / Hypothetical membrane protein
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMuraki, N. / Aono, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K15081 Japan
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Structural basis for the heme transfer reaction in heme uptake machinery from Corynebacteria.
Authors: Muraki, N. / Kitatsuji, C. / Okamoto, Y. / Uchida, T. / Ishimori, K. / Aono, S.
History
DepositionApr 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical membrane protein
B: Hypothetical membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5194
Polymers41,2862
Non-polymers1,2332
Water95553
1
A: Hypothetical membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2602
Polymers20,6431
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-18 kcal/mol
Surface area8450 Å2
MethodPISA
2
B: Hypothetical membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2602
Polymers20,6431
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-18 kcal/mol
Surface area8280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.120, 65.120, 181.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein Hypothetical membrane protein


Mass: 20643.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cgl0388 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NTB9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.4 M tri-sodium citrate, 0.1 M HEPES NaOH pH7.0, 3% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 13, 2014
RadiationMonochromator: Si (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→35.41 Å / Num. obs: 30290 / % possible obs: 99.87 % / Redundancy: 7.1 % / Biso Wilson estimate: 31.65 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0959 / Rpim(I) all: 0.0383 / Rrim(I) all: 0.1035 / Net I/σ(I): 11.01
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.6188 / Mean I/σ(I) obs: 3.03 / Num. unique obs: 3011 / CC1/2: 0.792 / Rpim(I) all: 0.2475 / Rrim(I) all: 0.6674 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2→35.409 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.55
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1512 4.99 %Random selection
Rwork0.1949 ---
obs0.1962 30279 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→35.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 0 86 53 2794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062810
X-RAY DIFFRACTIONf_angle_d0.9843845
X-RAY DIFFRACTIONf_dihedral_angle_d13.6041565
X-RAY DIFFRACTIONf_chiral_restr0.052418
X-RAY DIFFRACTIONf_plane_restr0.004502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.06450.31361210.27152590X-RAY DIFFRACTION100
2.0645-2.13830.29041210.25272603X-RAY DIFFRACTION100
2.1383-2.22390.29181510.23172580X-RAY DIFFRACTION100
2.2239-2.32510.27921560.23162612X-RAY DIFFRACTION100
2.3251-2.44770.29271250.2272573X-RAY DIFFRACTION100
2.4477-2.6010.28511420.22452604X-RAY DIFFRACTION100
2.601-2.80170.29691320.23782611X-RAY DIFFRACTION100
2.8017-3.08350.3191270.23392627X-RAY DIFFRACTION100
3.0835-3.52940.20871490.20252612X-RAY DIFFRACTION100
3.5294-4.44530.15691580.14872617X-RAY DIFFRACTION100
4.4453-35.41490.14991300.15462738X-RAY DIFFRACTION99
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)
10.8359-0.4438-0.51291.54261.19953.451-0.0505-0.1098-0.00810.13110.214-0.0935-0.06610.1037-0.04140.26070.1454-0.06180.4232-0.10310.3287-13.6705-7.483455.7332
21.09280.54530.83021.20160.69882.7899-0.26860.378-0.0859-0.21020.2618-0.0776-0.12970.2895-0.08940.2495-0.15070.0140.4918-0.05690.2912-11.5383-24.980711.3463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 39 through 218)
2X-RAY DIFFRACTION2(chain 'B' and resid 40 through 218)

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