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- PDB-4ymp: Crystal structure of the Bacillus anthracis Hal NEAT domain in co... -

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Basic information

Entry
Database: PDB / ID: 4ymp
TitleCrystal structure of the Bacillus anthracis Hal NEAT domain in complex with heme
ComponentsInternalin
KeywordsHeme-Binding Protein / Heme Binding Protein
Function / homology
Function and homology information


Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / Internalin
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsTorres, R. / Goulding, C.W.
CitationJournal: To Be Published
Title: Crystal structure of the Bacillus anthracis Hal NEAT domain in complex with heme
Authors: Torres, R. / Goulding, C.W.
History
DepositionMar 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Internalin
C: Internalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5584
Polymers30,3252
Non-polymers1,2332
Water0
1
A: Internalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7792
Polymers15,1621
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Internalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7792
Polymers15,1621
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.850, 84.850, 178.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: VAL / End label comp-ID: VAL

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1VALVALchain AAA10 - 12812 - 130
2ASPASPchain CCB12 - 12814 - 130

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Components

#1: Protein Internalin /


Mass: 15162.348 Da / Num. of mol.: 2 / Fragment: UNP residues 37-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: HYU01_03010 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: A0A075KLA4, UniProt: A0A1C7D116*PLUS
#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

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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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M ammonium sulfate, 0.1 M Bis Tris pH 5.5, 21% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2013
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→89.14 Å / Num. obs: 7129 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.184 / Net I/σ(I): 12.9
Reflection shellResolution: 3.15→3.37 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→46.206 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.326 709 10 %Random selection
Rwork0.2755 6378 --
obs0.2808 7087 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.02 Å2 / Biso mean: 111.5774 Å2 / Biso min: 57.39 Å2
Refinement stepCycle: final / Resolution: 3.15→46.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 86 0 1874
Biso mean--100.68 --
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041919
X-RAY DIFFRACTIONf_angle_d0.9742600
X-RAY DIFFRACTIONf_chiral_restr0.031272
X-RAY DIFFRACTIONf_plane_restr0.003314
X-RAY DIFFRACTIONf_dihedral_angle_d15.963703
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A916X-RAY DIFFRACTION11.831TORSIONAL
12C916X-RAY DIFFRACTION11.831TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1501-3.39330.36191370.350812261363
3.3933-3.73460.37931360.322612381374
3.7346-4.27470.34551390.295112531392
4.2747-5.38440.28231430.240212701413
5.3844-46.21050.32591540.265813911545
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)
15.8302-1.1880.88659.3621-3.09575.6179-0.5091-0.2375-0.3596-0.8020.1682-0.19140.86970.09910.5920.94760.11060.19380.7147-0.0720.8372-7.67320.376864.9717
29.7717-0.8052-2.04435.5546-0.17498.1669-0.2635-0.1194-0.4532-0.17310.0896-0.2135-0.15110.30910.40690.85390.0424-0.15190.40570.04150.901-7.970930.00272.4262
34.19894.765-3.99257.1444-1.68537.56320.0619-0.85430.3170.9108-0.15040.2180.19190.57410.03380.94330.0711-0.05040.550.15350.9901-12.004426.472573.5069
48.7094.4784-5.40495.4842-4.68354.2502-0.658-0.4797-0.6106-0.0067-0.2347-0.84621.29850.64491.00130.93240.124-0.00620.4944-0.00850.917-5.875221.410467.8682
52.99080.40740.23752.103-2.77783.86290.2625-0.9169-0.7469-0.4748-0.071-0.55620.67730.48650.21771.6699-0.0413-0.04160.46330.07241.23-21.469-5.516281.2121
63.18254.56330.29898.27742.09385.8167-0.4544-0.1755-0.1236-0.3331-0.73550.58611.5914-1.2873-0.12051.7518-0.32870.14470.7688-0.0430.9283-27.9107-5.047968.7493
72.01340.91010.63083.0204-2.19772.4910.54731.3012-1.254-0.9489-0.1158-0.40372.14191.58570.49811.89360.2776-0.20730.2023-0.04621.3919-19.9266-5.654575.8136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 35 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 73 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 111 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 128 )A0
5X-RAY DIFFRACTION5chain 'C' and (resid 12 through 51 )C0
6X-RAY DIFFRACTION6chain 'C' and (resid 52 through 84 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 85 through 128 )C0

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