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- PDB-5ihy: The crystal structure of Bacillus subtilis SeMet-YpgQ -

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Basic information

Entry
Database: PDB / ID: 5ihy
TitleThe crystal structure of Bacillus subtilis SeMet-YpgQ
ComponentsUncharacterized protein
KeywordsHYDROLASE / HD domain
Function / homologyHD-domain/PDEase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1910 / Cyclin A; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / NICKEL (II) ION / :
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJeon, Y.J. / Song, W.S. / Yoon, S.I.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structural and biochemical characterization of bacterial YpgQ protein reveals a metal-dependent nucleotide pyrophosphohydrolase
Authors: Jeon, Y.J. / Park, S.C. / Song, W.S. / Kim, O.H. / Oh, B.C. / Yoon, S.I.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9944
Polymers47,8762
Non-polymers1172
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-36 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.487, 53.087, 83.388
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 19
2115B2 - 18
1125A26 - 66
2125B26 - 66
1135A67 - 101
2135B67 - 105
1145A112 - 146
2145B106 - 146
1155A147 - 201
2155B147 - 201

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein Uncharacterized protein / Pyrophosphohydrolase


Mass: 23938.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BIS30_00575 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5CVW2
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 40% PEG 600, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97937 Å
DetectorType: ADSC Quantum Q270r / Detector: CCD / Date: Apr 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 14383 / % possible obs: 99.1 % / Redundancy: 7.2 % / Net I/σ(I): 29.4
Reflection shellResolution: 2.5→2.59 Å

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / ESU R: 0.764 / ESU R Free: 0.314 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26145 721 5 %RANDOM
Rwork0.21496 ---
obs0.21734 13621 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å2-1.29 Å2
2--1.26 Å20 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 2 16 2997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223050
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.9484130
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.355382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04724.15147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27315526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8621521
X-RAY DIFFRACTIONr_chiral_restr0.0690.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022284
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.321.51892
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.64223030
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.06231158
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8234.51097
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
168MEDIUM POSITIONAL0.180.5
169LOOSE POSITIONAL0.475
168MEDIUM THERMAL0.592
169LOOSE THERMAL0.5810
2164MEDIUM POSITIONAL0.240.5
2157LOOSE POSITIONAL0.445
2164MEDIUM THERMAL0.222
2157LOOSE THERMAL0.3310
3138MEDIUM POSITIONAL0.170.5
3104LOOSE POSITIONAL0.315
3138MEDIUM THERMAL0.392
3104LOOSE THERMAL0.5110
4139MEDIUM POSITIONAL0.170.5
4108LOOSE POSITIONAL0.535
4139MEDIUM THERMAL0.232
4108LOOSE THERMAL0.3410
5220MEDIUM POSITIONAL0.210.5
5234LOOSE POSITIONAL0.615
5220MEDIUM THERMAL0.22
5234LOOSE THERMAL0.3510
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 39 -
Rwork0.247 958 -
obs--96.61 %
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)
14.0407-0.3141.4830.6331-0.78361.3280.11260.2749-0.0185-0.0775-0.11640.00390.1310.14510.00370.08460.00860.05180.1015-0.01510.0398.153-7.35410.276
21.8557-1.6130.81223.4184-1.63051.78790.0461-0.1515-0.2626-0.1559-0.00720.05940.2535-0.0185-0.03890.1142-0.02160.05210.09520.03780.108428.052-25.45732.403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 204
2X-RAY DIFFRACTION2B2 - 201

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