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- PDB-7cy2: The open conformation of MSMEG_1954 from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 7cy2
TitleThe open conformation of MSMEG_1954 from Mycobacterium smegmatis
ComponentsABC1 family protein
KeywordsTRANSPORT PROTEIN / antibiotic binding / ADP binding
Function / homologyABC1 atypical kinase-like domain / ADCK3-like domain / ABC1 atypical kinase-like domain / Protein kinase-like domain superfamily / ABC1 family protein
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsZhang, Q. / Rao, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
CitationJournal: Front Microbiol / Year: 2021
Title: Conformational Changes in a Macrolide Antibiotic Binding Protein From Mycobacterium smegmatis Upon ADP Binding.
Authors: Zhang, Q. / Liu, X. / Liu, H. / Zhang, B. / Yang, H. / Mi, K. / Guddat, L.W. / Rao, Z.
History
DepositionSep 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0112
Polymers47,9151
Non-polymers961
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-18 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.006, 74.006, 167.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ABC1 family protein


Mass: 47915.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: MSMEG_1954
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0QTT2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe protein was expression with following sequence: ...The protein was expression with following sequence: MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKLEVLFQGPLGSPEFMSDIKRGSVARNAKLAGLAGGMAGRAALGFGKRLTGKSKDEVTAELMDKAAQQLFTVLGELKGGAMKVGQALSVMEAAIPEQYGKPYREALTKLQKDAPPLPAAKVHRVLDAQLGTKWRDRFSSFDDKPVASASIGQVHKGIWSDGREVAVKIQYPGADEALRADLKTIQRLVGVFKQLAPGADIQGVVDELTERTEMELDYRLEADNQRAFAKAYRNDPHFAVPAIIASAPKVVISEWMEGIPMSVIIREGTPEQRDLMGTRLTELTFGAPARLEMMHGDAHPGNFMLLPDGRMGVIDFGAVAPLPGGFPTSLGETIRLARDKNYDELLPTMERAGFLQKGQEVSIEEVEDMLRQYVDPIKVDVFHYNRKWLQKMAASQMDNSVAQIKMARSLDLPANLAIPLRVIASTVAICCQLDAHVPVKVIATELVPGFAEEAA However, the protein was degraded during crystallization and the exact sequence of the protein after degradation was not identified.

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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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium sulfate, 0.1M Tris (pH8.5), 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97876 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 12763 / % possible obs: 100 % / Redundancy: 24.5 % / Biso Wilson estimate: 44.45 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.025 / Rrim(I) all: 0.125 / Χ2: 1.123 / Net I/σ(I): 5.6 / Num. measured all: 312083
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.8121.11.7588110.8090.3751.7991.05399.9
2.81-2.8823.31.4998090.8710.3071.531.03499.8
2.88-2.9624.31.2948530.9070.2621.3211.019100
2.96-3.0524.40.9988140.9460.2031.0191.023100
3.05-3.15230.7988360.9570.1680.8161.019100
3.15-3.2626.20.5868330.9780.1140.5971.05100
3.26-3.3926.40.3978420.990.0770.4041.036100
3.39-3.5526.10.2678300.9950.0520.2731.16100
3.55-3.7325.90.2028520.9950.040.2061.152100
3.73-3.97250.148320.9980.0280.1431.16100
3.97-4.2723.90.0978490.9980.020.0991.049100
4.27-4.726.20.0768700.9990.0150.0780.967100
4.7-5.3825.30.0678610.9980.0130.0680.952100
5.38-6.7823.20.0638960.9980.0130.0651.153100
6.78-5022.60.0589750.9960.0130.061.96499.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YJZ

5yjz


Resolution: 2.75→49.94 Å / FOM work R set: 0.7872 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2873 612 5.03 %
Rwork0.2409 11551 -
obs0.2431 12163 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.78 Å2 / Biso mean: 55.75 Å2 / Biso min: 12.07 Å2
Refinement stepCycle: final / Resolution: 2.75→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 5 37 2536
Biso mean--98.63 37.42 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062551
X-RAY DIFFRACTIONf_angle_d1.1153461
X-RAY DIFFRACTIONf_chiral_restr0.046387
X-RAY DIFFRACTIONf_plane_restr0.005454
X-RAY DIFFRACTIONf_dihedral_angle_d14.79961
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7504-3.02720.34311510.3046237482
3.0272-3.46510.29581570.2752969100
3.4651-4.36530.28211500.22293027100
4.3653-49.940.2681540.22183181100
Refinement TLS params.Method: refined / Origin x: -30.8371 Å / Origin y: -9.2898 Å / Origin z: -12.7848 Å
111213212223313233
T0.3182 Å20.0238 Å20.1581 Å2-0.2064 Å2-0.0044 Å2--0.1816 Å2
L2.0989 °21.253 °2-0.4494 °2-4.5932 °20.5707 °2--1.4644 °2
S0.1018 Å °-0.1692 Å °0.043 Å °0.537 Å °-0.2679 Å °0.7211 Å °0.0608 Å °-0.337 Å °0.1124 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA98 - 437
2X-RAY DIFFRACTION1allA440 - 489

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