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- PDB-7sev: Crystal structure of E coli contaminant protein YadF co-purified ... -

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Basic information

Entry
Database: PDB / ID: 7sev
TitleCrystal structure of E coli contaminant protein YadF co-purified with a plant protein
ComponentsCarbonic anhydrase 2
KeywordsLYASE / YADF/P61517
Function / homology
Function and homology information


carbon utilization / carbonic anhydrase / carbonate dehydratase activity / protein homotetramerization / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Prokaryotic-type carbonic anhydrases signature 1. / Prokaryotic-type carbonic anhydrases signature 2. / Carbonic anhydrase, prokaryotic-like, conserved site / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase
Similarity search - Domain/homology
: / Carbonic anhydrase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChai, L. / Zhu, P. / Chai, J. / Pang, C. / Andi, B. / McsWeeney, S. / Shanklin, J. / Liu, Q.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Department of Energy (DOE, United States) United States
CitationJournal: Crystals / Year: 2021
Title: AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement
Authors: Chai, L. / Zhu, P. / Chai, J. / Pang, C. / Andi, B. / McSweeney, S. / Shanklin, J. / Liu, Q.
History
DepositionOct 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 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.pdbx_database_id_DOI / _citation.year / _citation_author.name
Revision 1.2Apr 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
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2353
Polymers25,1311
Non-polymers1052
Water1,20767
1
A: Carbonic anhydrase 2
hetero molecules

A: Carbonic anhydrase 2
hetero molecules

A: Carbonic anhydrase 2
hetero molecules

A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,94112
Polymers100,5234
Non-polymers4188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area16610 Å2
ΔGint-111 kcal/mol
Surface area32720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.500, 67.500, 85.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

21A-426-

HOH

31A-445-

HOH

41A-466-

HOH

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Components

#1: Protein Carbonic anhydrase 2 / / Carbonate dehydratase 2


Mass: 25130.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P61517, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.93 Å3/Da / Density % sol: 36.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium cacodylate, pH 6.8 and 1.8 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1.891 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.891 Å / Relative weight: 1
ReflectionResolution: 2.3→36.03 Å / Num. obs: 16710 / % possible obs: 100 % / Redundancy: 24 % / CC1/2: 0.995 / Net I/σ(I): 9.9
Reflection shellResolution: 2.3→2.36 Å / Num. unique obs: 665 / CC1/2: 0.812

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold AF-P61517-F1

Resolution: 2.3→36.03 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 757 4.53 %
Rwork0.2041 15953 -
obs0.2059 16710 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.55 Å2 / Biso mean: 38.9316 Å2 / Biso min: 24.23 Å2
Refinement stepCycle: final / Resolution: 2.3→36.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 2 67 1758
Biso mean--29.95 38.62 -
Num. residues----211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3-2.480.29591480.26323198
2.48-2.730.28371530.23943186
2.73-3.120.2661470.23653177
3.12-3.930.23781710.19643177
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)
12.3954-1.18172.95835.21650.16514.2737-0.11-0.3209-1.0410.09630.13130.23580.3399-0.1784-0.1260.5052-0.0543-0.01780.4177-0.02860.39912.98755.299630.6614
21.14722.31311.85214.86164.10173.7256-0.35490.34370.4058-0.5141-0.45350.9238-0.3503-0.64210.72390.3523-0.00010.03290.5865-0.03640.46347.23822.544439.1732
32.59150.23630.23372.0745-0.42422.09110.0416-0.2775-0.08570.3013-0.01860.11910.0439-0.1685-0.03760.2825-0.00040.03970.2638-0.00940.241421.793726.46155.5575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 21 )A2 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 42 )A22 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 212 )A43 - 212

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