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- PDB-7ylt: Structure of a bacteria protein -

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Basic information

Entry
Database: PDB / ID: 7ylt
TitleStructure of a bacteria protein
ComponentsPutative ABC transporter, substrate-binding protein
KeywordsMETAL BINDING PROTEIN / a bacteria protein / TRANSPORT PROTEIN
Function / homology: / Leucine-binding protein domain / Periplasmic binding protein / Periplasmic binding protein-like I / Putative ABC transporter, substrate-binding protein
Function and homology information
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, H. / Ma, Y.J. / Yu, G.M. / Li, X.Z.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Structure of a bacteria protein
Authors: Zhang, H. / Ma, Y.J. / Yu, G.M. / Li, X.Z.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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
B: Putative ABC transporter, substrate-binding protein
D: Putative ABC transporter, substrate-binding protein
C: Putative ABC transporter, substrate-binding protein
A: Putative ABC transporter, substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)153,5044
Polymers153,5044
Non-polymers00
Water9,404522
1
B: Putative ABC transporter, substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)38,3761
Polymers38,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Putative ABC transporter, substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)38,3761
Polymers38,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative ABC transporter, substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)38,3761
Polymers38,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Putative ABC transporter, substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)38,3761
Polymers38,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.775, 75.745, 119.706
Angle α, β, γ (deg.)85.600, 89.160, 89.370
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Putative ABC transporter, substrate-binding protein


Mass: 38375.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: VAPA_1c15920 / Production host: Escherichia coli (E. coli) / References: UniProt: T1X8R6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion
Details: Polyethylene glycol 3350, Tris, Cobalt(II) chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→48.67 Å / Num. obs: 52101 / % possible obs: 90.99 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.67 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.78
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 4716 / CC1/2: 0.968

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.20_4459phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 2.3→48.67 Å / SU ML: 0.2522 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.9203
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2275 2588 4.98 %
Rwork0.1863 49422 -
obs0.1883 52010 91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10737 0 0 522 11259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003310948
X-RAY DIFFRACTIONf_angle_d0.640714878
X-RAY DIFFRACTIONf_chiral_restr0.0431712
X-RAY DIFFRACTIONf_plane_restr0.00741923
X-RAY DIFFRACTIONf_dihedral_angle_d5.05991558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.28661380.22822556X-RAY DIFFRACTION86.9
2.34-2.390.23171270.21552395X-RAY DIFFRACTION79.46
2.39-2.440.28321430.22212815X-RAY DIFFRACTION90.43
2.44-2.50.26321400.21632801X-RAY DIFFRACTION94.87
2.5-2.560.28871360.20782860X-RAY DIFFRACTION94.6
2.56-2.630.27171630.20762879X-RAY DIFFRACTION94.15
2.63-2.710.24851490.20822778X-RAY DIFFRACTION93.51
2.71-2.80.27661450.21552841X-RAY DIFFRACTION92.91
2.8-2.90.27181470.21962770X-RAY DIFFRACTION92.63
2.9-3.010.25051560.21122753X-RAY DIFFRACTION91.54
3.01-3.150.23051160.20232731X-RAY DIFFRACTION89.84
3.15-3.320.21631680.20132668X-RAY DIFFRACTION88.05
3.32-3.520.2471430.19392410X-RAY DIFFRACTION81.67
3.52-3.80.2161560.17372896X-RAY DIFFRACTION95.46
3.8-4.180.23541530.16642891X-RAY DIFFRACTION95.21
4.18-4.780.16971550.14522830X-RAY DIFFRACTION94.73
4.78-6.020.1791360.16292793X-RAY DIFFRACTION91.39
6.02-48.670.18121170.15672755X-RAY DIFFRACTION90.69
Refinement TLS params.Method: refined / Origin x: 13.0277649281 Å / Origin y: 19.8693634351 Å / Origin z: 3.99097172731 Å
111213212223313233
T0.172065132666 Å20.0171998283761 Å20.0221988045065 Å2-0.187131139227 Å20.0164022506875 Å2--0.27591606755 Å2
L0.0726721197599 °20.0445585111703 °2-0.0372379244475 °2-0.204235802931 °2-0.0506081647089 °2--0.134093321962 °2
S0.0153659636075 Å °0.00315607180232 Å °0.0151504507911 Å °0.0122058863975 Å °-0.0289886908251 Å °0.0287673644006 Å °-0.0193582669947 Å °0.0195327298091 Å °0.0117521797452 Å °
Refinement TLS groupSelection details: all

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