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- PDB-7m58: Crystal structure of N1, a member of cis-3-chloroacrylic acid deh... -

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Basic information

Entry
Database: PDB / ID: 7m58
TitleCrystal structure of N1, a member of cis-3-chloroacrylic acid dehalogenase (cis-CaaD) family
ComponentsTautomerase_3 domain-containing protein
KeywordsHYDROLASE
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / Tautomerase_3 domain-containing protein
Function and homology information
Biological speciesCorynebacterium halotolerans YIM 70093 = DSM 44683 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMedellin, B.P. / Moreno, R.Y. / Zhang, Y.J.
Funding support4items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM-129331
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM-104896
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM125882
Robert A. Welch FoundationF-1778
CitationJournal: Biochemistry / Year: 2021
Title: Kinetic and Structural Analysis of Two Linkers in the Tautomerase Superfamily: Analysis and Implications.
Authors: Baas, B.J. / Medellin, B.P. / LeVieux, J.A. / Erwin, K. / Lancaster, E.B. / Johnson Jr., W.H. / Kaoud, T.S. / Moreno, R.Y. / de Ruijter, M. / Babbitt, P.C. / Zhang, Y.J. / Whitman, C.P.
History
DepositionMar 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tautomerase_3 domain-containing protein
B: Tautomerase_3 domain-containing protein
C: Tautomerase_3 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6816
Polymers48,3933
Non-polymers2883
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-98 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.362, 87.822, 120.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 143 / Label seq-ID: 1 - 143

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC

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Components

#1: Protein Tautomerase_3 domain-containing protein


Mass: 16131.092 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium halotolerans YIM 70093 = DSM 44683 (bacteria)
Gene: A605_05910
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: M1NLA4
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100mM Tris buffer pH 7.0, 35% PEG 3350, 200mM Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.446→50 Å / Num. obs: 15300 / % possible obs: 90.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.064 / Rrim(I) all: 0.144 / Χ2: 1.556 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.493.90.6497040.6450.3680.7530.61387
2.49-2.5440.5797210.640.3250.670.6687.8
2.54-2.594.10.5347320.7550.2890.6120.70687.2
2.59-2.644.30.5066980.7010.2740.580.75488.8
2.64-2.74.10.4197430.7790.2280.480.7787.9
2.7-2.7640.4327350.7860.2370.4970.79486.5
2.76-2.834.10.3587000.8690.1910.4090.84587.3
2.83-2.94.40.3097170.8970.1590.3510.90986.9
2.9-2.994.40.2977370.8930.1550.3380.9787.4
2.99-3.094.60.2537360.9270.130.2861.16389.1
3.09-3.24.50.227460.9490.1110.2481.33488.2
3.2-3.324.60.1837440.9670.0930.2071.39990.7
3.32-3.484.50.1517790.9730.0770.1711.70890.5
3.48-3.664.50.1337620.9740.0690.1512.1791.9
3.66-3.894.50.1117790.9870.0560.1252.19791.9
3.89-4.194.50.0998220.9890.0510.1122.46595.5
4.19-4.614.20.0848070.9890.0450.0962.86894.7
4.61-5.285.10.0828390.9910.040.0922.44398.1
5.28-6.655.80.0818750.9930.0350.0892.02499.2
6.65-506.10.0649240.9970.0260.072.21296.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N4G

3n4g


Resolution: 2.45→31.803 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 1528 10 %
Rwork0.1954 13750 -
obs0.2021 15278 90.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.63 Å2 / Biso mean: 33.8948 Å2 / Biso min: 16.28 Å2
Refinement stepCycle: final / Resolution: 2.45→31.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 15 69 3465
Biso mean--33.75 35.79 -
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013468
X-RAY DIFFRACTIONf_angle_d1.2474731
X-RAY DIFFRACTIONf_chiral_restr0.069534
X-RAY DIFFRACTIONf_plane_restr0.008618
X-RAY DIFFRACTIONf_dihedral_angle_d9.9552085
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2009X-RAY DIFFRACTION10.61TORSIONAL
12B2009X-RAY DIFFRACTION10.61TORSIONAL
13C2009X-RAY DIFFRACTION10.61TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.5250.33131200.2408108681
2.525-2.61520.30411340.2414120088
2.6152-2.71980.3041330.2352119588
2.7198-2.84360.35961300.2431117687
2.8436-2.99340.33681330.2393119988
2.9934-3.18080.30761370.2288123089
3.1808-3.42610.2961380.2097124091
3.4261-3.77040.22111400.1848125991
3.7704-4.31480.25461470.1662132296
4.3148-5.43180.21321520.1572136697
5.4318-31.8030.22441640.1826147798

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