PDB-8vkc: Crystal structure of dehaloperoxidase A in complex with substrate...

ID or keywords:

Entry

Database: PDB / ID: 8vkc

Title

Crystal structure of dehaloperoxidase A in complex with substrate 4-nitrophenol

Components

Dehaloperoxidase A

Keywords

OXIDOREDUCTASE / peroxidase / peroxigenase / oxidase / oxigenase / globin / heme cofactor / oxigen binding / hydrogen peroxide co-substrate / halphenol substrates

Function / homology

Function and homology information

oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function

Biological species

Amphitrite ornata (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.03 Å

Authors

Aktar, M.S. / de Serrano, V.S. / Ghiladi, R.A. / Franzen, S.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2024
Title: Structural Comparison of Substrate Binding Sites in Dehaloperoxidase A and B.
Authors: Aktar, M.S. / de Serrano, V. / Ghiladi, R.A. / Franzen, S.

History

Deposition	Jan 8, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 24, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8vkc.cif.gz	134.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8vkc.ent.gz		Display	PDB format
PDBx/mmJSON format	8vkc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8vkc_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8vkc_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8vkc_validation.xml.gz	15.3 KB	Display
Data in CIF	8vkc_validation.cif.gz	20.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vk/8vkc ftp://data.pdbj.org/pub/pdb/validation_reports/vk/8vkc	HTTPS FTP

-
Related structure data

Related structure data	8vkdC 8vskC 8vzrC 2qfkS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#206 - Feb 2017 Globin Evolution similarity (2) #116 - Aug 2009 Sulfotransferases similarity (1) #41 - May 2003 Hemoglobin similarity (1) #159 - Mar 2013 Erythrocruorin similarity (2) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#206 - Feb 2017
Globin Evolution
similarity (2)
#116 - Aug 2009
Sulfotransferases
similarity (1)
#41 - May 2003
Hemoglobin
similarity (1)
#159 - Mar 2013
Erythrocruorin
similarity (2)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#142 - Oct 2011
PDB Pioneers
similarity (1)

Deposited unit

AAA: Dehaloperoxidase A

BBB: Dehaloperoxidase A

hetero molecules

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

1

AAA: Dehaloperoxidase A

hetero molecules

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

2

BBB: Dehaloperoxidase A

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.824, 67.936, 68.276
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 2 molecules AAABBB

#1: Protein	Dehaloperoxidase A Mass: 15548.597 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amphitrite ornata (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NAV8

-
Non-polymers , 5 types, 111 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NPO / P-NITROPHENOL Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₅NO₃
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.93 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: MPEG 2000, ammonium sulfate, sodium cacodylate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Sep 25, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.03→30.43 Å / Num. obs: 16983 / % possible obs: 93.05 % / Redundancy: 3.7 % / CC_1/2: 0.98 / Net I/σ(I): 12.4
Reflection shell	Resolution: 2.03→2.083 Å / Num. unique obs: 973 / CC_1/2: 0.314

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2QFK

2qfk

Resolution: 2.03→30.43 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.901 / SU B: 15.382 / SU ML: 0.183 / Cross valid method: FREE R-VALUE / ESU R Free: 0.233
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2745	841	4.952 %
R_work	0.1541	16142	-
all	0.16	-	-
obs	-	16983	93.047 %

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: 28.825 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.758 Å²	-0 Å²	0 Å²
2-	-	0.632 Å²	-0 Å²
3-	-	-	0.127 Å²

Refinement step

Cycle: LAST / Resolution: 2.03→30.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2182	0	127	103	2412

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	2576
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	2354
X-RAY DIFFRACTION	r_angle_refined_deg	1.572	1.705	3519
X-RAY DIFFRACTION	r_angle_other_deg	1.38	1.625	5420
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.015	5	322
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.09	21.831	142
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.324	15	454
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.425	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	304
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3072
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	680
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	677
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	2143
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	1245
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1058
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.2	112
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.096	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.231	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.183	0.2	85
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.131	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	3.825	2.815	1204
X-RAY DIFFRACTION	r_mcbond_other	3.826	2.815	1203
X-RAY DIFFRACTION	r_mcangle_it	4.785	4.228	1536
X-RAY DIFFRACTION	r_mcangle_other	4.784	4.229	1537
X-RAY DIFFRACTION	r_scbond_it	4.494	3.153	1372
X-RAY DIFFRACTION	r_scbond_other	4.458	3.141	1359
X-RAY DIFFRACTION	r_scangle_it	5.628	4.589	1977
X-RAY DIFFRACTION	r_scangle_other	5.62	4.572	1959
X-RAY DIFFRACTION	r_lrange_it	5.998	33.754	3188
X-RAY DIFFRACTION	r_lrange_other	5.995	33.719	3183
X-RAY DIFFRACTION	r_rigid_bond_restr	2.193	3	4930

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.03-2.083	0.307	66	0.234	973	X-RAY DIFFRACTION	79.2525
2.083-2.14	0.433	47	0.206	1131	X-RAY DIFFRACTION	89.3101
2.14-2.202	0.364	43	0.183	1075	X-RAY DIFFRACTION	90.38
2.202-2.27	0.372	56	0.193	1067	X-RAY DIFFRACTION	91.3751
2.27-2.344	0.287	63	0.154	1038	X-RAY DIFFRACTION	92.8331
2.344-2.426	0.274	65	0.136	993	X-RAY DIFFRACTION	92.8885
2.426-2.517	0.247	47	0.143	975	X-RAY DIFFRACTION	92.3216
2.517-2.62	0.291	48	0.133	958	X-RAY DIFFRACTION	93.321
2.62-2.736	0.319	33	0.142	916	X-RAY DIFFRACTION	93.4055
2.736-2.869	0.318	56	0.14	881	X-RAY DIFFRACTION	94.8381
2.869-3.023	0.294	42	0.128	852	X-RAY DIFFRACTION	95.2077
3.023-3.206	0.277	37	0.138	798	X-RAY DIFFRACTION	93.0881
3.206-3.426	0.279	31	0.14	765	X-RAY DIFFRACTION	94.2012
3.426-3.699	0.239	39	0.156	725	X-RAY DIFFRACTION	98.0745
3.699-4.05	0.223	37	0.142	690	X-RAY DIFFRACTION	99.7257
4.05-4.524	0.25	51	0.12	633	X-RAY DIFFRACTION	100
4.524-5.216	0.254	29	0.138	554	X-RAY DIFFRACTION	100
5.216-6.37	0.216	18	0.197	494	X-RAY DIFFRACTION	100
6.37-8.931	0.179	19	0.183	392	X-RAY DIFFRACTION	99.5157
8.931-30.43	0.366	14	0.198	232	X-RAY DIFFRACTION	96.4706

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AAABBB

-
Non-polymers , 5 types, 111 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AAABBB

-Non-polymers , 5 types, 111 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AAABBB

-
Non-polymers , 5 types, 111 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi