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- PDB-6jsc: Crystal structure of the H434A variant of the C-terminal domain o... -

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Basic information

Entry
Database: PDB / ID: 6jsc
TitleCrystal structure of the H434A variant of the C-terminal domain of HtaA from Corynebacterium glutamicum
ComponentsHypothetical membrane protein
KeywordsHEME-BINDING PROTEIN / heme / heme transport
Function / homologyHtaa / Htaa / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / Hypothetical membrane protein
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)37,6488
Polymers36,3232
Non-polymers1,3256
Water3,081171
1
A: Hypothetical membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8244
Polymers18,1621
Non-polymers6623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-18 kcal/mol
Surface area7660 Å2
MethodPISA
2
B: Hypothetical membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8244
Polymers18,1621
Non-polymers6623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-18 kcal/mol
Surface area7790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.040, 43.150, 199.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical membrane protein


Mass: 18161.576 Da / Num. of mol.: 2 / Mutation: H434A
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 / Plasmid: pET22b / 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: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 4.5 M HCOONA, HEPES pH7.0, 7% sucrose

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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: Apr 23, 2017
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: 1.4→36.2 Å / Num. obs: 66461 / % possible obs: 98.19 % / Redundancy: 7.4 % / Biso Wilson estimate: 13.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0665 / Rpim(I) all: 0.0263 / Rrim(I) all: 0.0716 / Net I/σ(I): 17.73
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.624 / Num. unique obs: 6437 / CC1/2: 0.884 / Rpim(I) all: 0.243 / Rrim(I) all: 0.67 / % possible all: 96.87

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JSA

6jsa


Resolution: 1.4→36.194 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 3323 5 %Random selection
Rwork0.1813 ---
obs0.1824 66461 98.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→36.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 90 171 2673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052639
X-RAY DIFFRACTIONf_angle_d1.1663638
X-RAY DIFFRACTIONf_dihedral_angle_d17.208894
X-RAY DIFFRACTIONf_chiral_restr0.09391
X-RAY DIFFRACTIONf_plane_restr0.004483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3997-1.41960.25651320.24682507X-RAY DIFFRACTION96
1.4196-1.44080.24511360.22472573X-RAY DIFFRACTION97
1.4408-1.46340.22031330.20782542X-RAY DIFFRACTION97
1.4634-1.48730.21371380.20362606X-RAY DIFFRACTION97
1.4873-1.5130.23321320.19362520X-RAY DIFFRACTION97
1.513-1.54050.21111370.19072595X-RAY DIFFRACTION97
1.5405-1.57010.22191360.17722578X-RAY DIFFRACTION97
1.5701-1.60220.21941350.18142575X-RAY DIFFRACTION98
1.6022-1.6370.2141370.1762593X-RAY DIFFRACTION98
1.637-1.67510.18021350.16972576X-RAY DIFFRACTION98
1.6751-1.7170.1741390.16772633X-RAY DIFFRACTION98
1.717-1.76340.18591370.16262602X-RAY DIFFRACTION98
1.7634-1.81530.19131370.17432606X-RAY DIFFRACTION98
1.8153-1.87390.21761390.17772650X-RAY DIFFRACTION99
1.8739-1.94090.18971390.1762633X-RAY DIFFRACTION99
1.9409-2.01860.2021370.17082609X-RAY DIFFRACTION99
2.0186-2.11040.20981390.16442638X-RAY DIFFRACTION99
2.1104-2.22170.19181410.16872670X-RAY DIFFRACTION99
2.2217-2.36080.18591400.18022670X-RAY DIFFRACTION99
2.3608-2.54310.18351420.19252696X-RAY DIFFRACTION99
2.5431-2.79890.19541420.20692708X-RAY DIFFRACTION99
2.7989-3.20370.21581430.20292718X-RAY DIFFRACTION100
3.2037-4.03550.21331460.17112757X-RAY DIFFRACTION99
4.0355-36.20630.19271510.16792883X-RAY DIFFRACTION98
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)
10.9301-0.1043-0.60511.01160.17712.29070.04350.01420.0407-0.03490.00660.0472-0.1199-0.0441-0.04270.0609-0.000400.0646-0.00290.09453.2465-4.8528-25.3752
20.9055-0.329-0.11240.92110.08921.93560.0064-0.0217-0.09770.00850.03350.0030.26270.0253-0.0250.08020.0042-0.0060.0741-0.00570.108422.0513-25.4493-25.2063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 364 through 530)
2X-RAY DIFFRACTION2(chain 'B' and resid 364 through 531)

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