PDB-5uq4: Crystal structure of Heme-Degrading Protein Rv3592 from Mycobacte...

ID or keywords:

Entry

Database: PDB / ID: 5uq4

Title

Crystal structure of Heme-Degrading Protein Rv3592 from Mycobacterium tuberculosis - heme free with cleaved protein

Components

Monooxygenase

Keywords

OXIDOREDUCTASE / Structural Genomics / Center For Structural Genomics Of Infectious Disease / heme-degrading protein / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

heme oxygenase (mycobilin-producing) / heme oxygenase (decyclizing) activity / heme catabolic process / peptidoglycan-based cell wall / heme binding / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.201 Å

Authors

Chang, C. / Chhor, G. / Jedrzejczak, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal structure of Heme-Degrading Protein Rv3592 from Mycobacterium tuberculosis - heme free with cleaved protein.
Authors: Chang, C. / Chhor, G. / Jedrzejczak, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Feb 6, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5uq4.cif.gz	81.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5uq4.ent.gz	59.8 KB	Display	PDB format
PDBx/mmJSON format	5uq4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5uq4_validation.pdf.gz	436.7 KB	Display	wwPDB validaton report
Full document	5uq4_full_validation.pdf.gz	438.3 KB	Display
Data in XML	5uq4_validation.xml.gz	9.1 KB	Display
Data in CIF	5uq4_validation.cif.gz	11.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uq/5uq4 ftp://data.pdbj.org/pub/pdb/validation_reports/uq/5uq4	HTTPS FTP

-
Related structure data

Related structure data	3hx9S S: Starting model for refinement
Similar structure data	3wi3-3 3iij-d 3iil-d 6lan-d 4wvz-1 2dos-d 4tlf-2 5x07-1 3coa-2 4fak-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP55742

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Monooxygenase

B: Monooxygenase

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	38.134, 38.134, 238.638
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

Details

THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

#1: Protein	Monooxygenase Mass: 11470.872 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: LH57_19585 / Plasmid: pMCSG7 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: I6X7R2, UniProt: P9WKH3*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Monooxygenase

Mass: 11470.872 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: LH57_19585 / Plasmid: pMCSG7
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: I6X7R2, UniProt: P9WKH3*PLUS

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.09 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M magnesium chloride, 0.1M bi-Tris, 25% PEG3350

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97924 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2011

Radiation

Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97924 Å / Relative weight: 1

Reflection twin

Operator: h,-h-k,-l / Fraction: 0.4

Reflection

Resolution: 2.2→50 Å / Num. obs: 10093 / % possible obs: 99.9 % / Redundancy: 10.1 % / R_merge(I) obs: 0.099 / R_pim(I) all: 0.032 / R_rim(I) all: 0.104 / Χ²: 1.028 / Net I/σ(I): 9.8 / Num. measured all: 101734

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.2-2.24	5.4	1.099	496	0.772	0.46	1.196	0.908	100
2.24-2.28	6.7	1.065	500	0.822	0.406	1.142	0.897	100
2.28-2.32	7.9	0.928	485	0.856	0.332	0.987	0.903	100
2.32-2.37	8.5	0.881	542	0.902	0.307	0.934	0.931	100
2.37-2.42	9.1	0.744	477	0.931	0.25	0.786	0.908	100
2.42-2.48	9.7	0.762	497	0.932	0.251	0.803	0.917	100
2.48-2.54	10.3	0.674	524	0.974	0.218	0.709	0.928	100
2.54-2.61	10.6	0.7	481	0.938	0.225	0.736	0.922	100
2.61-2.69	10.9	0.428	507	0.983	0.136	0.449	1.015	100
2.69-2.77	11	0.36	510	0.984	0.114	0.378	1.01	100
2.77-2.87	11.2	0.283	483	0.989	0.089	0.297	1.023	100
2.87-2.99	11.2	0.223	518	0.992	0.07	0.234	1.082	100
2.99-3.12	11.1	0.162	498	0.992	0.051	0.17	1.128	100
3.12-3.29	11.2	0.124	509	0.993	0.039	0.13	1.037	100
3.29-3.49	11.2	0.089	528	0.997	0.028	0.094	1.08	100
3.49-3.76	11.2	0.069	483	0.997	0.021	0.072	1.198	100
3.76-4.14	11.2	0.065	499	0.998	0.02	0.068	1.253	99.8
4.14-4.74	11.1	0.057	530	0.996	0.018	0.06	1.296	100
4.74-5.97	11.1	0.048	495	0.997	0.015	0.051	1.037	99.8
5.97-50	10.8	0.043	531	0.997	0.014	0.045	0.838	99.1

-
Processing

Software

Name	Version	Classification
PHENIX	dev_2650	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.22	data extraction
HKL-3000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3HX9

3hx9

Resolution: 2.201→33.025 Å / Cross valid method: FREE R-VALUE / σ(F): 12.15 / Phase error: 31.65 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2231	494	5.33 %
R_work	0.1721	8741	-
obs	0.1761	9273	93.62 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 92.19 Å² / B_iso mean: 31.0368 Å² / B_iso min: 6.06 Å²

Refinement step

Cycle: final / Resolution: 2.201→33.025 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1357	0	0	59	1416
B_iso mean	-	-	-	39.79	-
Num. residues	-	-	-	-	176

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	1393
X-RAY DIFFRACTION	f_angle_d	0.469	1892
X-RAY DIFFRACTION	f_chiral_restr	0.042	202
X-RAY DIFFRACTION	f_plane_restr	0.004	251
X-RAY DIFFRACTION	f_dihedral_angle_d	6.694	810

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 4

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.2053-2.4268	0.2544	98	0.2004	1749	1847	72
2.4268-2.7767	0.3176	118	0.1837	2344	2462	95
2.7767-3.494	0.2322	123	0.178	2348	2471	95
3.494-17.7069	0.1885	151	0.1586	2300	2451	94

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.006	-0.0014	-0.0061	0.0034	0.0037	0.011	-0.0081	-0.0021	0.0015	-0.0076	-0.0113	0.0129	-0.0098	0.0013	-0.007	0.0301	-0.0755	-0.0024	0.1311	-0.0346	0.1068	-2.8887	12.5443	4.044
2	0.0093	0.0027	-0.0003	0.0046	0.0024	0.0018	-0.0024	0.0031	-0.0016	-0.0029	-0.0037	0.001	-0.0004	-0.0021	0	0.312	-0.035	0.0221	0.3938	0.0033	0.3644	-20.9271	9.7786	-4.5617
3	0.0007	0.0007	0.0007	0.0014	0.0013	0.001	0.0043	0.0051	-0.0079	-0.0112	0.0051	0.0094	0.0154	-0.0204	0	0.1534	-0.1237	0.0031	0.2699	-0.0115	0.1813	-9.9982	3.0523	-7.9754
4	0.001	-0.0001	-0.0007	-0.0001	0.0006	0.0008	0.0118	0.0144	-0.01	-0.008	0.0167	-0.01	0.0352	0.0184	-0	0.0669	-0.0116	0.0163	0.1942	-0.031	0.1633	0.9586	2.9885	-0.939
5	0.0026	-0.001	0.0002	0.0011	0.0008	0.0013	-0.0057	-0.0054	0.0029	-0.0028	0.0038	0.0004	-0.0026	-0.0137	0	0.1597	-0.0309	-0.0259	0.2423	0.0201	0.2418	-18.4662	8.3594	6.9712
6	0.0109	0.0125	0.0093	0.0198	0.0174	0.0268	0.0332	0.0003	0.017	-0.0154	0.0011	-0.0021	-0.0089	0.0251	0.0458	0.0422	-0.078	0.0509	0.1858	0.004	0.1749	1.3813	11.412	-1.9925
7	0.0027	0.002	0.0003	0.0037	0.004	0.0098	0.0059	0.0074	0.01	0.005	0.0073	0.0091	-0.0026	0.0103	0.0155	0.0548	-0.1187	-0.0338	0.087	0.0349	0.1995	0.4004	11.3894	10.5522
8	0.0041	0.0008	-0.0026	0.0047	-0.005	0.0057	-0.0046	0.0126	-0.0016	0.0016	0.0049	0.0013	-0.0001	-0.0122	0.0001	0.1615	-0.164	-0.0153	0.0913	0.0088	0.1382	-9.1018	8.5067	15.0826
9	0.0005	0.0001	0.0017	0.0018	-0.0018	0.0033	-0.006	-0.0186	-0.0014	0.0031	0.0097	0.0092	0.0241	0.0216	-0	0.2152	-0.0961	-0.0478	0.1547	0.0415	0.1164	-0.142	7.6869	25.3526
10	-0.0004	0.0003	0.0007	0.0014	-0.0003	0.0011	-0.0017	-0.0104	-0.0279	-0.0072	-0.0078	0.0033	0.023	-0.0026	0	0.1038	-0.0328	0.0273	0.0488	-0.0167	0.0991	-3.4779	0.1194	17.346
11	0.0007	0.0013	-0.0021	0.0003	0.0012	0.0054	0.0019	0.0058	0.0098	0.0072	-0.0036	-0.002	0.0125	-0.0198	-0.013	0.1009	-0.1689	0.029	0.0963	0.0545	0.1483	-9.2775	5.8762	17.7117
12	0.0015	0.0005	0.0019	0.0018	0.0004	0.0023	-0.011	0.0035	-0.0179	0.0043	0.0349	-0.0042	0.0031	-0.0274	0	0.1177	-0.0764	0.0321	0.1692	-0.0345	0.218	-10.5784	3.72	7.5905

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 10 )	A	1 - 10
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 11 through 15 )	A	11 - 15
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 16 through 28 )	A	16 - 28
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 29 through 42 )	A	29 - 42
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 43 through 49 )	A	43 - 49
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 50 through 87 )	A	50 - 87
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 88 through 99 )	A	88 - 99
8	X-RAY DIFFRACTION	8	chain 'B' and (resid -1 through 15 )	B	-1 - 15
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 16 through 31 )	B	16 - 31
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 32 through 42 )	B	32 - 42
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 43 through 86 )	B	43 - 86
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 87 through 100 )	B	87 - 100

-
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://pdbjlvh1.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

-
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

-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

-
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