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- PDB-5ie9: Crystal structure of the Bacillus-conserved MazG protein, a nucle... -

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Basic information

Entry
Database: PDB / ID: 5ie9
TitleCrystal structure of the Bacillus-conserved MazG protein, a nucleotide pyrophosphohydrolase
ComponentsNucleotide pyrophosphohydrolase
KeywordsHYDROLASE / MazG / nucleoside triphosphate pyrophosphohydrolase
Function / homology
Function and homology information


NTP pyrophosphohydrolase MazG-related, YpjD / NTP pyrophosphohydrolase MazG, putative catalytic core / MazG nucleotide pyrophosphohydrolase domain / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / Hypothetical Transcriptional Regulatory Protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKim, M. / Hong, M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
The ministry of Science, ICT & Future planning2013R1A1A1008707 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Crystal structure of the Bacillus-conserved MazG protein, a nucleotide pyrophosphohydrolase.
Authors: Kim, M.I. / Hong, M.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector ...citation / diffrn_detector / pdbx_struct_oper_list / reflns
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation / _reflns.d_resolution_high / _reflns.d_resolution_low
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleotide pyrophosphohydrolase
B: Nucleotide pyrophosphohydrolase
C: Nucleotide pyrophosphohydrolase
D: Nucleotide pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3598
Polymers48,1394
Non-polymers2204
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11670 Å2
ΔGint-138 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.578, 90.578, 97.056
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Nucleotide pyrophosphohydrolase


Mass: 12034.801 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 20-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: TQ94_28555 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A0A3VU53, UniProt: Q813T0*PLUS
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

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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: 4.78 Å3/Da / Density % sol: 74.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1mM sodium cacodylate pH 6.5, 1M sodium citrate

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Data collection

DiffractionMean temperature: 83 K / Ambient temp details: N2
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: May 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.77→30 Å / % possible obs: 98.7 % / Redundancy: 3 %
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / % possible all: 89.4

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GTA

2gta


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.911 / SU B: 24.82 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.274 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1059 4.9 %RANDOM
Rwork0.2217 ---
obs0.2232 20632 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.22 Å2 / Biso mean: 46 Å2 / Biso min: 52.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å2-0 Å2
2---0.22 Å2-0 Å2
3---0.72 Å2
Refinement stepCycle: final / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 4 0 2952
Biso mean--90.65 --
Num. residues----375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192984
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9593998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7385367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25725.556153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.60315554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3191514
X-RAY DIFFRACTIONr_chiral_restr0.0860.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022234
X-RAY DIFFRACTIONr_mcbond_it0.9554.5991491
X-RAY DIFFRACTIONr_mcangle_it1.6776.891849
X-RAY DIFFRACTIONr_scbond_it1.3784.6471493
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 81 -
Rwork0.315 1505 -
all-1586 -
obs--100 %
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)
12.42031.57420.25438.4916-2.50221.21130.0277-0.3513-0.10580.84570.03410.2503-0.0124-0.003-0.06190.8204-0.23440.05550.57240.13440.1865-23.082-25.36614.669
212.9206-10.71131.92515.47520.45371.79110.3147-0.5173-0.5923-0.252-0.20170.81520.2149-0.4739-0.1130.1417-0.18080.00960.3313-0.03220.0838-28.397-15.491-1.721
37.0733-0.02422.34238.20590.79273.68930.0115-0.1671-0.00790.5935-0.0337-0.17580.03160.16860.02220.3572-0.3213-0.00780.35660.00560.0073-21.146-14.3959.435
40.01640.09030.3071.11453.429410.67890.0574-0.0505-0.0176-0.2412-0.0016-0.0387-0.5225-0.2554-0.05580.8342-0.2702-0.02060.5765-0.07390.6962-10.8018.33615.294
56.2496-0.1120.04634.25871.56664.7568-0.3072-0.38970.24870.76420.0196-0.5509-0.4652-0.22230.28770.6795-0.3134-0.04710.4901-0.12820.2412-22.105-0.71514.552
610.214-8.6422-1.951514.722-0.22631.91330.1184-0.58330.48640.027-0.1198-0.9801-0.27290.52670.00140.1168-0.1782-0.02690.35370.06030.0849-15.721-11.465-1.06
75.62050.2298-1.097110.584-1.77683.5009-0.0481-0.1270.11620.63770.1210.5671-0.071-0.08-0.07290.3699-0.31110.03070.388-0.02890.0491-26.261-11.82910.085
83.95051.4211-10.84650.5656-4.029730.1520.0168-0.25590.1616-0.14730.0491-0.0350.40260.5071-0.06590.8478-0.21550.08190.63530.03040.959-35.28-35.95616.463
916.598-5.06944.79296.4896-0.19647.9868-0.05011.00350.2159-0.6484-0.3569-0.52040.43450.30060.40710.1877-0.08220.12590.7228-0.01050.0899-11.753-18.386-27.623
106.2403-5.97110.643113.64394.53753.4261-0.55650.19290.48650.23210.9646-1.1262-0.26110.7317-0.40810.2165-0.2071-0.01610.46880.0280.1704-16.927-10.844-10.965
115.1448-0.72531.42645.5672-0.55792.97030.21370.7926-0.0561-0.0715-0.29720.16830.02720.01070.08350.0984-0.1510.02340.7094-0.03860.0318-22.784-14.366-20.92
125.14521.052410.93730.76042.653923.61550.24280.0216-0.07-0.29830.1958-0.52460.12880.1289-0.43870.54110.0140.05750.7803-0.05530.7942-48.925-13.317-28.359
138.93111.8682-1.62675.7865-0.42136.7307-0.00440.5452-0.1655-0.4583-0.24460.4791-0.2005-0.28850.24910.1791-0.0989-0.11750.82710.05830.0961-33.533-7.263-26.601
144.6672-6.4801-1.277719.5683-0.98122.8143-0.24910.1383-0.31510.05450.47390.51530.347-0.4879-0.22480.1126-0.17370.01030.307-0.01680.0864-27.58-16.645-10.227
156.9489-1.1024-2.47646.9826-1.42074.45390.23510.7250.1815-0.3076-0.1962-0.1764-0.1688-0.2272-0.03880.1131-0.1672-0.01840.66450.03510.0396-23.078-10.467-21.575
161.51291.1189-4.73690.8431-3.547314.96910.08760.12990.13810.00330.12950.0377-0.0815-0.4126-0.21710.34890.09840.1660.7829-0.08060.63182.173-12.794-27.224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 25
2X-RAY DIFFRACTION2A26 - 49
3X-RAY DIFFRACTION3A50 - 95
4X-RAY DIFFRACTION4A96 - 103
5X-RAY DIFFRACTION5B1 - 25
6X-RAY DIFFRACTION6B26 - 63
7X-RAY DIFFRACTION7B64 - 96
8X-RAY DIFFRACTION8B97 - 103
9X-RAY DIFFRACTION9C1 - 23
10X-RAY DIFFRACTION10C24 - 49
11X-RAY DIFFRACTION11C50 - 96
12X-RAY DIFFRACTION12C97 - 103
13X-RAY DIFFRACTION13D1 - 25
14X-RAY DIFFRACTION14D26 - 49
15X-RAY DIFFRACTION15D50 - 95
16X-RAY DIFFRACTION16D96 - 103

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