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- PDB-7v5h: VcOrn native structure with N terminal tag -

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Basic information

Entry
Database: PDB / ID: 7v5h
TitleVcOrn native structure with N terminal tag
ComponentsOligoribonuclease
KeywordsHYDROLASE / VcOrn / Active pocket / N terminal tag.
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / cytoplasm
Similarity search - Function
Oligoribonuclease / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhang, J. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800627 China
National Natural Science Foundation of China (NSFC)31870053 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structure of oligoribonuclease from Vibrio cholerae O1 El Tor with bound peptide.
Authors: Zhang, J. / Sun, L. / Zhang, Q. / Bartlam, M.
History
DepositionAug 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Oligoribonuclease


Theoretical massNumber of molelcules
Total (without water)22,7121
Polymers22,7121
Non-polymers00
Water2,666148
1
A: Oligoribonuclease

A: Oligoribonuclease


Theoretical massNumber of molelcules
Total (without water)45,4232
Polymers45,4232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area4680 Å2
ΔGint-26 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.522, 84.522, 55.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Oligoribonuclease


Mass: 22711.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Gene: orn, VC_0341 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9KV17, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.6
Details: 2.0M sodium formate, 0.1M sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 25735 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 23.04 Å2 / Rpim(I) all: 0.041 / Net I/σ(I): 25.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 2.76 / Num. unique obs: 1259 / Rpim(I) all: 0.395 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N6A

6n6a


Resolution: 1.7→27.67 Å / SU ML: 0.1525 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 20.3454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1926 1917 7.71 %
Rwork0.1732 22946 -
obs0.1748 24863 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 0 148 1672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721558
X-RAY DIFFRACTIONf_angle_d0.96712105
X-RAY DIFFRACTIONf_chiral_restr0.0634231
X-RAY DIFFRACTIONf_plane_restr0.0075269
X-RAY DIFFRACTIONf_dihedral_angle_d6.1826201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.29731230.22541508X-RAY DIFFRACTION89.52
1.74-1.790.22131290.19941529X-RAY DIFFRACTION91.4
1.79-1.840.23371270.20531551X-RAY DIFFRACTION91.95
1.84-1.90.23751280.1971555X-RAY DIFFRACTION93.6
1.9-1.970.22881340.1851611X-RAY DIFFRACTION95.72
1.97-2.050.20491400.17071628X-RAY DIFFRACTION97.57
2.05-2.140.18861300.16541651X-RAY DIFFRACTION98.29
2.14-2.250.19421440.1631666X-RAY DIFFRACTION98.53
2.25-2.390.19021410.17391655X-RAY DIFFRACTION98.63
2.39-2.580.20231410.17631678X-RAY DIFFRACTION98.91
2.58-2.840.22051390.19581688X-RAY DIFFRACTION99.46
2.84-3.250.1891450.16971720X-RAY DIFFRACTION99.89
3.25-4.090.16921460.16251710X-RAY DIFFRACTION100
4.09-27.670.17681500.16471796X-RAY DIFFRACTION99.59
Refinement TLS params.Method: refined / Origin x: 57.3275569127 Å / Origin y: 35.3102681131 Å / Origin z: 8.50648304712 Å
111213212223313233
T0.140033589068 Å2-0.0210632476841 Å2-0.00897136378163 Å2-0.177413873276 Å20.00230860218918 Å2--0.159429222635 Å2
L0.965813045788 °2-0.063737947679 °20.0161922732766 °2-1.1433496665 °20.00163995294456 °2--1.48908405056 °2
S-0.0403472992183 Å °-0.0677815467609 Å °-0.0670391256364 Å °-0.0137690551093 Å °0.0210329010324 Å °-0.0605391913528 Å °0.0581966011081 Å °0.0129910274414 Å °0.02452284342 Å °
Refinement TLS groupSelection details: all

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