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- PDB-4ohn: Crystal structure of an ABC uptake transporter substrate binding ... -

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Basic information

Entry
Database: PDB / ID: 4ohn
TitleCrystal structure of an ABC uptake transporter substrate binding protein from Streptococcus pneumoniae with Bound Histidine
ComponentsABC transporter substrate-binding protein
KeywordsTRANSPORT PROTEIN / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / ABC transporter substrate-binding protein - glutamine transport / Histidine
Function / homology
Function and homology information


Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / HISTIDINE / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å
AuthorsBrunzelle, J.S. / Wawrzak, W. / Yim, Y. / Kudritska, M. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of an ABC uptake transporter substrate binding protein from Streptococcus pneumoniae with Bound Histidine
Authors: Brunzelle, J.S. / Wawrzak, W. / Yim, Y. / Kudritska, M. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases
History
DepositionJan 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9314
Polymers28,6571
Non-polymers2743
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.125, 87.125, 70.949
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein ABC transporter substrate-binding protein


Mass: 28656.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: Canada MDR_19A / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: A0A0H2UKY8*PLUS
#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8K 30% w/v Na Acetate 0.2M Bis-Tris 0.1M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.28756 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2013 / Details: Double Silicone 111 crystalBi-morph Mirrors
RadiationMonochromator: Double Silicone 111 Crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28756 Å / Relative weight: 1
ReflectionResolution: 1.37→37.12 Å / Num. all: 64061 / Num. obs: 64061 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4 / Scaling rejects: 313
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.37-1.426.70.6832.741332615698
5.31-37.1211.30.05235.613090116099.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.29data scaling
MOLREPphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
BLU-MAXdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q2C

2q2c


Resolution: 1.37→33.31 Å / FOM work R set: 0.9262 / SU ML: 0.12 / Isotropic thermal model: Isotropic / Cross valid method: Thoughout / σ(F): 1.34 / Phase error: 13.71 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1527 3245 5.07 %Random
Rwork0.1369 ---
all0.1377 64008 --
obs0.1377 64008 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.97 Å2 / Biso mean: 18.85 Å2 / Biso min: 6.41 Å2
Refinement stepCycle: LAST / Resolution: 1.37→33.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 19 304 2263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092201
X-RAY DIFFRACTIONf_angle_d1.233004
X-RAY DIFFRACTIONf_chiral_restr0.08321
X-RAY DIFFRACTIONf_plane_restr0.005404
X-RAY DIFFRACTIONf_dihedral_angle_d13.378812
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.37-1.39050.27571540.27692550270498
1.3905-1.41220.27631370.23012592272998
1.4122-1.43530.20451480.19262581272998
1.4353-1.46010.23231310.18032614274599
1.4601-1.48660.19681270.163226502777100
1.4866-1.51520.1711640.155826212785100
1.5152-1.54620.17531320.150526572789100
1.5462-1.57980.15651330.148726462779100
1.5798-1.61650.17621380.148826502788100
1.6165-1.6570.1661490.138726232772100
1.657-1.70180.13691460.13726592805100
1.7018-1.75180.14681580.130126132771100
1.7518-1.80840.15491280.128626612789100
1.8084-1.8730.13351370.132626542791100
1.873-1.9480.17251420.133326292771100
1.948-2.03660.14951400.131926762816100
2.0366-2.1440.14571550.129826082763100
2.144-2.27830.14451380.128626812819100
2.2783-2.45410.15011480.127926462794100
2.4541-2.7010.12521340.136226582792100
2.701-3.09160.13611500.132626732823100
3.0916-3.89410.14321190.125226942813100
3.8941-33.31960.14111370.124127272864100
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)
16.4219-1.83330.63975.7675-3.69072.99740.08230.3414-0.5591-0.5819-0.08690.23630.3641-0.0984-0.08690.1650.0229-0.01430.1823-0.09420.154916.006220.698115.8809
21.7809-0.4432-0.31591.26690.35440.90670.01310.15350.0083-0.0169-0.0183-0.03030.0444-0.0330.01460.07240.00710.00340.1026-0.01080.071810.975334.42725.6431
30.7421-0.9116-1.41911.88142.0032.8006-0.0958-0.0837-0.06590.13410.03070.04690.20050.13140.03710.09940.0243-0.02050.09990.00830.09210.057734.562345.0668
41.40530.2418-0.66461.9058-0.1182.1385-0.0157-0.0976-0.10470.076-0.0751-0.02310.1446-0.03590.0840.0766-0.0157-0.00520.09920.00310.0658-1.745237.296146.819
50.5154-0.6328-0.76181.4641.81262.5567-0.0125-0.0279-0.02330.04340.0701-0.05610.02090.105-0.05560.06690.0024-0.01360.088-0.00120.084210.939339.919641.7612
62.07-0.5718-0.18063.90210.89830.4850.0057-0.19430.18790.17330.0396-0.17670.04530.0481-0.03610.10350.0161-0.0160.1311-0.03310.12725.381134.449730.7103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 38 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 109 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 143 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 196 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 197 through 237 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 238 through 272 )A0

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