PDB-2h3r: Crystal structure of ORF52 from Murid herpesvirus 4 (MuHV-4) (Mur...

ID or keywords:

Entry

Database: PDB / ID: 2h3r

Title

Crystal structure of ORF52 from Murid herpesvirus 4 (MuHV-4) (Murine gammaherpesvirus 68). Northeast Structural Genomics Consortium target MhR28B.

Components

Hypothetical protein BQLF2

Hypothesis

Keywords

STRUCTURAL PROTEIN / NESG / MHR28B /

Structural Genomics / PSI-2 /

Protein Structure Initiative / Northeast Structural Genomics Consortium

Function / homology

Herpesvirus BLRF2 / Herpesvirus BLRF2 protein / YejL-like / YejL-like / Orthogonal Bundle / Mainly Alpha / 52 protein

Function and homology information

Biological species

Murid herpesvirus 4 (Murine herpesvirus 68)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.7 Å

Authors

Benach, J. / Chen, Y. / Seetharaman, J. / Janjua, H. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Ho, C.K. / Acton, T.B. / Montelione, G.T. ...

Citation

Journal: To be Published
Title: Crystal structure of ORF52 from Murid herpesvirus 4 (MuHV-4) (Murine gammaherpesvirus 68). Northeast Structural Genomics Consortium target MhR28B.
Authors: Benach, J. / Chen, Y. / Seetharaman, J. / Janjua, H. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Ho, C.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)

History

Deposition	May 23, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 15, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2h3r.cif.gz	77.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2h3r.ent.gz	62.2 KB	Display	PDB format
PDBx/mmJSON format	2h3r.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h3/2h3r ftp://data.pdbj.org/pub/pdb/validation_reports/h3/2h3r	HTTPS FTP

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Related structure data

Similar structure data	6kk9-3 2ol6-d 2i5z-d 2pi3-d 6kk9-2 2ol8-d 6j48-d 2oa5-d 3aum-d 6j5p-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: MHR28B

Similar structure data

Other databases

TargetDB: MHR28B

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hypothetical protein BQLF2

B: Hypothetical protein BQLF2

C: Hypothetical protein BQLF2

D: Hypothetical protein BQLF2

50.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hypothetical protein BQLF2

B: Hypothetical protein BQLF2

defined by author&software
25 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Hypothetical protein BQLF2

D: Hypothetical protein BQLF2

defined by author&software
25 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Hypothetical protein BQLF2

D: Hypothetical protein BQLF2

C: Hypothetical protein BQLF2

D: Hypothetical protein BQLF2

defined by software
50.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

A: Hypothetical protein BQLF2

B: Hypothetical protein BQLF2

A: Hypothetical protein BQLF2

B: Hypothetical protein BQLF2

defined by software
50.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	54.926, 49.240, 88.915
Angle α, β, γ (deg.)	90.00, 105.61, 90.00
Int Tables number	3
Space group name H-M	P121

#1: Protein	Hypothetical protein BQLF2 / Hypothesis / Hypothetical protein GAMMAHV.ORF52 Mass: 12517.789 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68) Genus: Rhadinovirus / Strain: 68 strain WUMS / Gene: BQLF2, GAMMAHV.ORF52 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Magic / References: UniProt: P88989
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Hypothetical protein BQLF2 /

Hypothesis / Hypothetical protein GAMMAHV.ORF52

Mass: 12517.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Murid herpesvirus 4 (Murine herpesvirus 68)
Genus: Rhadinovirus

/ Strain: 68 strain WUMS / Gene: BQLF2, GAMMAHV.ORF52 / Plasmid: pET21 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Magic / References: UniProt: P88989

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.81 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 80% PEG 400, 100mM MOPS, 100mM NaNO3, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	NSLS	X4A	1	0.97912,0.97947,0.96790,0.97930
SYNCHROTRON	NSLS	X4A	2	0.9793

Detector

Type	ID	Detector	Date
ADSC QUANTUM 4	1	CCD	Apr 24, 2006
ADSC QUANTUM 4	2	CCD	May 9, 2006

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SI 111 CHANNEL	MAD	M	x-ray	1
2	SI 111 CHANNEL	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97912	1
2	0.97947	1
3	0.9679	1
4	0.9793	1

Reflection

D res high: 2.35 Å / D res low: 20 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs	% possible obs
4.2	1	13.1	164307	0.094	1.37	39303	99.6
4.2	2	11.6	162423	0.089	1.16	38883	99.7
3.5	3	6.8	136808	0.088	1.13	39588	99.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.31	20	94.5	1	0.076	2.471	3.8
5.04	6.31	98.9	1	0.082	2.002	4.1
4.41	5.04	99.3	1	0.077	2.048	4
4.01	4.41	99.8	1	0.076	2.007	4.1
3.72	4.01	99.9	1	0.075	1.813	4.2
3.51	3.72	99.8	1	0.077	1.565	4.2
3.33	3.51	99.9	1	0.086	1.528	4.3
3.19	3.33	99.9	1	0.093	1.326	4.3
3.06	3.19	100	1	0.104	1.219	4.3
2.96	3.06	100	1	0.116	1.18	4.3
2.87	2.96	100	1	0.133	1.162	4.3
2.79	2.87	100	1	0.173	1.104	4.3
2.71	2.79	99.9	1	0.183	1.05	4.3
2.65	2.71	99.9	1	0.229	1.037	4.3
2.59	2.65	100	1	0.219	0.989	4.3
2.53	2.59	100	1	0.264	1.033	4.2
2.48	2.53	99.9	1	0.3	1.014	4.2
2.43	2.48	99.9	1	0.36	1.045	4.1
2.39	2.43	100	1	0.363	1.021	4.1
2.35	2.39	100	1	0.443	1.02	4
6.31	20	95	2	0.068	1.731	4
5.04	6.31	99.7	2	0.065	1.428	4.2
4.41	5.04	99.9	2	0.066	1.662	4.2
4.01	4.41	99.9	2	0.067	1.632	4.2
3.72	4.01	99.9	2	0.067	1.405	4.3
3.51	3.72	99.9	2	0.072	1.277	4.3
3.33	3.51	99.9	2	0.085	1.196	4.3
3.19	3.33	100	2	0.098	1.073	4.3
3.06	3.19	99.9	2	0.118	1.021	4.3
2.96	3.06	100	2	0.141	1.029	4.3
2.87	2.96	100	2	0.161	0.983	4.3
2.79	2.87	100	2	0.231	0.996	4.3
2.71	2.79	99.9	2	0.26	0.987	4.3
2.65	2.71	99.9	2	0.33	0.997	4.2
2.59	2.65	99.9	2	0.351	0.972	4.1
2.53	2.59	100	2	0.41	0.969	4.1
2.48	2.53	99.9	2	0.436	0.974	4
2.43	2.48	99.9	2	0.625	0.958	3.9
2.39	2.43	99.9	2	0.576	0.94	3.9
2.35	2.39	99.9	2	0.705	0.96	3.9
6.31	20	97.7	3	0.05	1.766	3.2
5.04	6.31	99.4	3	0.064	1.458	3.4
4.41	5.04	99.8	3	0.062	1.53	3.4
4.01	4.41	99.9	3	0.071	1.595	3.5
3.72	4.01	99.9	3	0.089	1.456	3.5
3.51	3.72	99.9	3	0.112	1.255	3.6
3.33	3.51	99.9	3	0.141	1.109	3.6
3.19	3.33	99.9	3	0.195	1.058	3.6
3.06	3.19	100	3	0.256	1.009	3.6
2.96	3.06	99.9	3	0.344	1.011	3.6
2.87	2.96	99.9	3	0.447	0.993	3.6
2.79	2.87	99.9	3	0.681	0.987	3.6
2.71	2.79	100	3	0.746	0.954	3.5
2.65	2.71	99.9	3		0.963	3.5
2.59	2.65	99.8	3		0.93	3.4
2.53	2.59	99.7	3		0.941	3.4
2.48	2.53	99.6	3		0.916	3.3
2.43	2.48	99.2	3		0.891	3.3
2.39	2.43	99.4	3		0.889	3.2
2.35	2.39	99.2	3		0.938	3.1

Reflection

Resolution: 2.7→50 Å / Num. obs: 23521 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / R_merge(I) obs: 0.086 / Net I/σ(I): 13.8

Reflection shell

Resolution: 2.7→2.8 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.394 / % possible all: 93.2

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SnB		phasing
RESOLVE		phasing
CNS		refinement
PDB_EXTRACT	2	data extraction
ADSC		data collection

Refinement

Method to determine structure:

MAD / Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.295	1862	7.6 %	RANDOM
R_work	0.275	-	-	-
obs	0.275	20535	83.4 %	-
all	-	24620	-	-

Solvent computation

B_sol: 43.91 Å²

Displacement parameters

B_iso mean: 40.81 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.874 Å²	0 Å²	-8.638 Å²
2-	-	-8.554 Å²	0 Å²
3-	-	-	12.428 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2769	0	0	10	2779

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_bond_d
X-RAY DIFFRACTION	c_bond_d_na
X-RAY DIFFRACTION	c_bond_d_prot
X-RAY DIFFRACTION	c_angle_d
X-RAY DIFFRACTION	c_angle_d_na
X-RAY DIFFRACTION	c_angle_d_prot
X-RAY DIFFRACTION	c_angle_deg
X-RAY DIFFRACTION	c_angle_deg_na
X-RAY DIFFRACTION	c_angle_deg_prot
X-RAY DIFFRACTION	c_dihedral_angle_d
X-RAY DIFFRACTION	c_dihedral_angle_d_na
X-RAY DIFFRACTION	c_dihedral_angle_d_prot
X-RAY DIFFRACTION	c_improper_angle_d
X-RAY DIFFRACTION	c_improper_angle_d_na
X-RAY DIFFRACTION	c_improper_angle_d_prot
X-RAY DIFFRACTION	c_mcbond_it	1.054	1.5
X-RAY DIFFRACTION	c_mcangle_it	1.813	2
X-RAY DIFFRACTION	c_scbond_it	2.077	2
X-RAY DIFFRACTION	c_scangle_it	3.051	2.5

Refine LS restraints NCS

NCS model details: RESTRAINED

LS refinement shell

Resolution: 2.7→2.72 Å / Total num. of bins used: 37 /

	R_factor	Num. reflection
R_free	0.352	29
R_work	0.303	436

Xplor file

Refine-ID	Serial no	Param file	Topol file
X-RAY DIFFRACTION	1	PROTEIN_REP.PAR	protein.top
X-RAY DIFFRACTION	2	WATER_REP.PARAM	water.top

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