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- PDB-7cz2: The complex structure of MSMEG_1954-ADP from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 7cz2
TitleThe complex structure of MSMEG_1954-ADP 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 / nucleotide binding / Protein kinase-like domain superfamily / metal ion binding / ADENOSINE-5'-DIPHOSPHATE / ABC1 family protein
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 7, 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)48,5155
Polymers47,9151
Non-polymers5994
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-32 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.650, 83.650, 100.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-848-

HOH

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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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M calcium acetate hydrate, 0.1M sodium cacodylate trihydrate (pH6.5), 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 38277 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.023 / Rrim(I) all: 0.072 / Χ2: 0.979 / Net I/σ(I): 7.8 / Num. measured all: 377947
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8310.11.09818700.8080.3611.1570.992100
1.83-1.8610.10.8819070.890.2890.9261.013100
1.86-1.9100.70919030.9290.2350.7471.00599.9
1.9-1.94100.58818770.9320.1950.6191.025100
1.94-1.989.90.46719040.9750.1560.4931.018100
1.98-2.039.30.37918610.9710.1310.4011.007100
2.03-2.089.40.30119210.9740.1030.3181.05100
2.08-2.1310.30.23618620.9890.0770.2481.01100
2.13-2.210.20.219080.990.0660.2111.008100
2.2-2.2710.10.17318950.9910.0570.1820.977100
2.27-2.359.90.14618890.9950.0490.1540.954100
2.35-2.449.50.12519080.9930.0420.1320.93100
2.44-2.559.50.10119170.9940.0350.1070.839100
2.55-2.6910.20.08819040.9960.0290.0920.797100
2.69-2.8610.20.06919030.9970.0230.0721.163100
2.86-3.08100.06119360.9970.0210.0650.946100
3.08-3.399.40.05419270.9980.0190.0570.835100
3.39-3.8810.30.04919500.9980.0160.0510.803100
3.88-4.889.40.04719620.9980.0160.050.969100
4.88-509.60.0620730.9940.020.0641.238100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YJZ

5yjz


Resolution: 1.8→38.66 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.709 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 1878 5.1 %RANDOM
Rwork0.1913 ---
obs0.193 35129 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.01 Å2 / Biso mean: 27.533 Å2 / Biso min: 4.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.8→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 35 316 2776
Biso mean--18.35 34.23 -
Num. residues----313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132540
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172405
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.6463449
X-RAY DIFFRACTIONr_angle_other_deg1.4021.5775570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1855315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30521.579133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88715424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3061521
X-RAY DIFFRACTIONr_chiral_restr0.0910.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022820
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02518
LS refinement shellResolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 81 -
Rwork0.253 1688 -
all-1769 -
obs--63.61 %

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