PDB-9dyt: Acanthamoeba Polyphaga Mimivirus R699

ID or keywords:

Entry

Database: PDB / ID: 9dyt

Title

Acanthamoeba Polyphaga Mimivirus R699

Components

R699

Keywords

VIRAL PROTEIN / R699

Function / homology

procollagen-lysine 5-dioxygenase activity / : / : / Uncharacterized protein R699

Function and homology information

Biological species

Acanthamoeba polyphaga mimivirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Richards, S.J. / Buhlheller, C. / Kim, J.S. / Chen, T. / Wu, J. / Guo, H.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Cancer Institute (NIH/NCI)	R00CA225633	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	R37CA278989	United States

Citation

Journal: To Be Published
Title: Acanthamoeba Polyphaga Mimivirus R699
Authors: Richards, S.J. / Buhlheller, C. / Kim, J.S. / Chen, T. / Wu, J. / Guo, H.

History

Deposition	Oct 14, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 11, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9dyt.cif.gz	211 KB	Display	PDBx/mmCIF format
PDB format	pdb9dyt.ent.gz	160.3 KB	Display	PDB format
PDBx/mmJSON format	9dyt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dy/9dyt ftp://data.pdbj.org/pub/pdb/validation_reports/dy/9dyt	HTTPS FTP

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Related structure data

Related structure data	9dzsC 9e92C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: R699

B: R699

hetero molecules

107 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: R699

hetero molecules

defined by author
53.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: R699

hetero molecules

defined by author
53.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.821, 121.696, 72.690
Angle α, β, γ (deg.)	90.000, 118.589, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: VAL / End label comp-ID: VAL / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 9 - 455 / Label seq-ID: 12 - 458

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	R699 Mass: 53317.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UNV6
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.63 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Protein/cofactor mix: 30mg/ml R699, 2mM MnCl2. mother liquor: 0.2 M Ammonium formate, 20% (w/v) PEG 3350 The ratio of mix and mother liquor was at 1:1.

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Data collection

Diffraction	Mean temperature: 110 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→61.383 Å / Num. obs: 97211 / % possible obs: 98.8 % / Redundancy: 6.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.079 / Net I/σ(I): 10.7
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.908 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4789 / CC_1/2: 0.864 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
DIALS	3.8.0	data collection
xia2	3.8.0	data reduction
Aimless	0.7.8	data scaling
PHENIX	1.20.1	phasing
PHASER	2.8.3	phasing
Coot	0.9.8.92	model building
REFMAC	5.8.0425	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→61.383 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.956 / SU B: 3.473 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.118 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2199	4915	5.059 %
R_work	0.1895	92246	-
all	0.191	-	-
obs	-	97161	98.669 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 33.623 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.213 Å²	-0 Å²	-0.825 Å²
2-	-	3.899 Å²	0 Å²
3-	-	-	-2.016 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→61.383 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7220	0	2	506	7728

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	7462
X-RAY DIFFRACTION	r_angle_refined_deg	1.536	1.826	10091
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.752	5	890
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.096	5	32
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.821	10	1345
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.976	10	380
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	1072
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5720
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	3226
X-RAY DIFFRACTION	r_nbtor_refined	0.317	0.2	5073
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	479
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.213	0.2	84
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.129	0.2	23
X-RAY DIFFRACTION	r_mcbond_it	2.724	3.114	3527
X-RAY DIFFRACTION	r_mcangle_it	3.834	5.577	4410
X-RAY DIFFRACTION	r_scbond_it	3.695	3.451	3935
X-RAY DIFFRACTION	r_scangle_it	5.565	6.17	5675
X-RAY DIFFRACTION	r_lrange_it	6.925	37.233	11434
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.094	0.05	14638

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09432	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09432	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.8-1.847	0.322	379	0.303	6831	0.304	7259	0.914	0.92	99.325	0.288
1.847-1.897	0.32	351	0.276	6688	0.279	7091	0.927	0.941	99.2667	0.259
1.897-1.952	0.3	350	0.262	6458	0.264	6864	0.942	0.948	99.1842	0.242
1.952-2.012	0.277	339	0.252	6268	0.253	6675	0.937	0.955	98.9813	0.232
2.012-2.078	0.294	365	0.235	6095	0.238	6515	0.946	0.963	99.1558	0.218
2.078-2.151	0.25	306	0.216	5764	0.218	6244	0.957	0.968	97.2133	0.197
2.151-2.232	0.252	256	0.217	5528	0.218	6036	0.959	0.97	95.8251	0.2
2.232-2.323	0.244	241	0.204	5563	0.206	5846	0.964	0.974	99.2816	0.188
2.323-2.426	0.252	281	0.196	5278	0.198	5589	0.961	0.977	99.4632	0.182
2.426-2.545	0.234	271	0.205	5034	0.206	5321	0.965	0.976	99.6993	0.194
2.545-2.682	0.258	237	0.195	4852	0.198	5111	0.961	0.978	99.5695	0.188
2.682-2.844	0.257	229	0.199	4528	0.201	4798	0.959	0.976	99.1455	0.197
2.844-3.04	0.214	186	0.191	4294	0.192	4564	0.971	0.978	98.1595	0.196
3.04-3.283	0.186	193	0.186	3800	0.186	4176	0.979	0.98	95.6178	0.195
3.283-3.595	0.209	222	0.179	3648	0.181	3890	0.972	0.983	99.4859	0.192
3.595-4.018	0.2	222	0.165	3278	0.168	3528	0.981	0.985	99.2063	0.184
4.018-4.636	0.17	151	0.142	2944	0.143	3110	0.985	0.989	99.5177	0.168
4.636-5.67	0.156	118	0.139	2486	0.14	2630	0.988	0.99	99.0114	0.165
5.67-7.985	0.224	161	0.184	1799	0.187	2053	0.979	0.985	95.47	0.213
7.985-61.383	0.154	57	0.179	1110	0.177	1171	0.99	0.982	99.6584	0.219

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