PDB-3eoo: 2.9A crystal structure of methyl-isocitrate lyase from Burkholder...

ID or keywords:

Entry

Database: PDB / ID: 3eoo

Title

2.9A crystal structure of methyl-isocitrate lyase from Burkholderia pseudomallei

Components

Methylisocitrate lyase

Keywords

LYASE / BURKHOLDERIA / PSEUDOMALLEI / METHYL-ISOCITRATE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID

Function / homology

Phosphoenolpyruvate-binding domains / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / :

Function and homology information

Biological species

Burkholderia pseudomallei 1655 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structures of isocitrate lyase from Brucella melitensis
Authors: SSGCID

History

Deposition	Sep 28, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 21, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3eoo.cif.gz	808.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3eoo.ent.gz	680.7 KB	Display	PDB format
PDBx/mmJSON format	3eoo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3eoo_validation.pdf.gz	548.3 KB	Display	wwPDB validaton report
Full document	3eoo_full_validation.pdf.gz	663.7 KB	Display
Data in XML	3eoo_validation.xml.gz	154 KB	Display
Data in CIF	3eoo_validation.cif.gz	205.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eo/3eoo ftp://data.pdbj.org/pub/pdb/validation_reports/eo/3eoo	HTTPS FTP

-
Related structure data

Related structure data	3eolC 3eom 3eon C: citing same article (ref.)
Similar structure data	1oqf-1 4lmr-1 1ceq-1 2dua-1 1cet-1 1mum-1 1gv0-1 1pze-1 4plw-d 4b7u-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: BupsA.00014.b

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Methylisocitrate lyase

B: Methylisocitrate lyase

C: Methylisocitrate lyase

D: Methylisocitrate lyase

E: Methylisocitrate lyase

F: Methylisocitrate lyase

G: Methylisocitrate lyase

H: Methylisocitrate lyase

I: Methylisocitrate lyase

J: Methylisocitrate lyase

K: Methylisocitrate lyase

L: Methylisocitrate lyase

M: Methylisocitrate lyase

N: Methylisocitrate lyase

O: Methylisocitrate lyase

P: Methylisocitrate lyase

512 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Methylisocitrate lyase

B: Methylisocitrate lyase

C: Methylisocitrate lyase

D: Methylisocitrate lyase

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

2

E: Methylisocitrate lyase

F: Methylisocitrate lyase

M: Methylisocitrate lyase

N: Methylisocitrate lyase

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

3

G: Methylisocitrate lyase

H: Methylisocitrate lyase

I: Methylisocitrate lyase

J: Methylisocitrate lyase

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

4

K: Methylisocitrate lyase

L: Methylisocitrate lyase

O: Methylisocitrate lyase

P: Methylisocitrate lyase

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

Unit cell

Length a, b, c (Å)	163.807, 172.404, 179.277
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	GLY	GLY	A	A	10 - 110	11 - 111
2	1	GLY	GLY	GLY	GLY	B	B	10 - 110	11 - 111
3	1	GLY	GLY	GLY	GLY	C	C	10 - 110	11 - 111
4	1	GLY	GLY	GLY	GLY	D	D	10 - 110	11 - 111
5	1	GLY	GLY	GLY	GLY	E	E	10 - 110	11 - 111
6	1	GLY	GLY	GLY	GLY	F	F	10 - 110	11 - 111
7	1	GLY	GLY	GLY	GLY	G	G	10 - 110	11 - 111
8	1	GLY	GLY	GLY	GLY	H	H	10 - 110	11 - 111
9	1	GLY	GLY	GLY	GLY	I	I	10 - 110	11 - 111
10	1	GLY	GLY	GLY	GLY	J	J	10 - 110	11 - 111
11	1	GLY	GLY	GLY	GLY	K	K	10 - 110	11 - 111
12	1	GLY	GLY	GLY	GLY	L	L	10 - 110	11 - 111
13	1	GLY	GLY	GLY	GLY	M	M	10 - 110	11 - 111
14	1	GLY	GLY	GLY	GLY	N	N	10 - 110	11 - 111
15	1	GLY	GLY	GLY	GLY	O	O	10 - 110	11 - 111
16	1	GLY	GLY	GLY	GLY	P	P	10 - 110	11 - 111
1	2	VAL	VAL	ALA	ALA	A	A	140 - 265	141 - 266
2	2	VAL	VAL	ALA	ALA	B	B	140 - 265	141 - 266
3	2	VAL	VAL	ALA	ALA	C	C	140 - 265	141 - 266
4	2	VAL	VAL	ALA	ALA	D	D	140 - 265	141 - 266
5	2	VAL	VAL	ALA	ALA	E	E	140 - 265	141 - 266
6	2	VAL	VAL	ALA	ALA	F	F	140 - 265	141 - 266
7	2	VAL	VAL	ALA	ALA	G	G	140 - 265	141 - 266
8	2	VAL	VAL	ALA	ALA	H	H	140 - 265	141 - 266
9	2	VAL	VAL	ALA	ALA	I	I	140 - 265	141 - 266
10	2	VAL	VAL	ALA	ALA	J	J	140 - 265	141 - 266
11	2	VAL	VAL	ALA	ALA	K	K	140 - 265	141 - 266
12	2	VAL	VAL	ALA	ALA	L	L	140 - 265	141 - 266
13	2	VAL	VAL	ALA	ALA	M	M	140 - 265	141 - 266
14	2	VAL	VAL	ALA	ALA	N	N	140 - 265	141 - 266
15	2	VAL	VAL	ALA	ALA	O	O	140 - 265	141 - 266
16	2	VAL	VAL	ALA	ALA	P	P	140 - 265	141 - 266

#1: Protein	Methylisocitrate lyase / E.C.4.1.3.30 Mass: 32009.436 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei 1655 (bacteria) Strain: 1710B Gene: BURPS1655_C0444, BURPS1710B_2458, BURPS1710b_3237, MSRB, prpB Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2H5R7, methylisocitrate lyase
Has protein modification	Y

#1: Protein

Methylisocitrate lyase / E.C.4.1.3.30

Mass: 32009.436 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia pseudomallei 1655 (bacteria)
Strain: 1710B
Gene: BURPS1655_C0444, BURPS1710B_2458, BURPS1710b_3237, MSRB, prpB
Plasmid: AVA0421 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2H5R7, methylisocitrate lyase

Has protein modification

Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.23 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion / pH: 6.5 Details: 25% PEG 3350, 0.1M BIS-TRIS pH 6.5, 0.2M NaCl, VAPOR DIFFUSION, temperature 289K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS

Radiation

Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.7→48.28 Å / Num. obs: 137453 / % possible obs: 98.6 % / Redundancy: 4.78 % / R_merge(I) obs: 0.126 / Χ²: 0.95 / Scaling rejects: 4966

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	Χ²	% possible all
2.7-2.8	4.64	0.534	2	64263	13684	1.37	99.2
2.8-2.91	4.68	0.48	2.2	64326	13619	1.28	99.1
2.91-3.04	4.67	0.386	2.8	64832	13747	1.2	99.1
3.04-3.2	4.7	0.306	3.5	64893	13678	1.11	99
3.2-3.4	4.69	0.226	4.7	64971	13718	1.01	99.1
3.4-3.66	4.7	0.159	6.3	64942	13716	0.9	98.8
3.66-4.03	4.77	0.107	8.8	65863	13728	0.79	98.7
4.03-4.62	4.93	0.087	10.6	68012	13743	0.71	98.5
4.62-5.81	5.07	0.074	12.2	70166	13796	0.65	98
5.81-48.28	4.96	0.051	15.3	69750	14024	0.57	97

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 39.69 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.7 Å	48.28 Å
Translation	2.7 Å	48.28 Å

-
Processing

Software

Name	Version	Classification
d*TREK	9.7L	data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→48 Å / Cor.coef. F_o:F_c: 0.912 / Cor.coef. F_o:F_c free: 0.859 / WR_factor R_free: 0.275 / WR_factor R_work: 0.213 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.751 / SU B: 23.654 / SU ML: 0.423 / SU R_free: 0.509 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.299	5514	5 %	RANDOM
R_work	0.237	-	-	-
all	0.24	111006	-	-
obs	0.24	111006	98.46 %	-

Solvent computation

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

Displacement parameters

B_iso max: 90.59 Å² / B_iso mean: 48.512 Å² / B_iso min: 21.33 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.15 Å²	0 Å²	0 Å²
2-	-	0.55 Å²	0 Å²
3-	-	-	-0.41 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	34623	0	0	0	34623

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	35183
X-RAY DIFFRACTION	r_angle_refined_deg	1.522	1.962	47673
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.499	5	4580
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.593	23.935	1530
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.111	15	5727
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.781	15	256
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	5452
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	26728
X-RAY DIFFRACTION	r_nbd_refined	0.239	0.2	16562
X-RAY DIFFRACTION	r_nbtor_refined	0.311	0.2	24309
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	634
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.228	0.2	183
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.2	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	0.483	1.5	23218
X-RAY DIFFRACTION	r_mcangle_it	0.87	2	36109
X-RAY DIFFRACTION	r_scbond_it	1.136	3	13413
X-RAY DIFFRACTION	r_scangle_it	1.85	4.5	11564

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	908	TIGHT POSITIONAL	0.05	0.05
2	B	908	TIGHT POSITIONAL	0.05	0.05
3	C	908	TIGHT POSITIONAL	0.05	0.05
4	D	908	TIGHT POSITIONAL	0.04	0.05
5	E	908	TIGHT POSITIONAL	0.05	0.05
6	F	908	TIGHT POSITIONAL	0.05	0.05
7	G	908	TIGHT POSITIONAL	0.04	0.05
8	H	908	TIGHT POSITIONAL	0.05	0.05
9	I	908	TIGHT POSITIONAL	0.05	0.05
10	J	908	TIGHT POSITIONAL	0.05	0.05
11	K	908	TIGHT POSITIONAL	0.04	0.05
12	L	908	TIGHT POSITIONAL	0.05	0.05
13	M	908	TIGHT POSITIONAL	0.05	0.05
14	N	908	TIGHT POSITIONAL	0.06	0.05
15	O	908	TIGHT POSITIONAL	0.05	0.05
16	P	908	TIGHT POSITIONAL	0.05	0.05
1	A	780	MEDIUM POSITIONAL	0.42	0.5
2	B	780	MEDIUM POSITIONAL	0.39	0.5
3	C	780	MEDIUM POSITIONAL	0.39	0.5
4	D	780	MEDIUM POSITIONAL	0.35	0.5
5	E	780	MEDIUM POSITIONAL	0.45	0.5
6	F	780	MEDIUM POSITIONAL	0.42	0.5
7	G	780	MEDIUM POSITIONAL	0.38	0.5
8	H	780	MEDIUM POSITIONAL	0.35	0.5
9	I	780	MEDIUM POSITIONAL	0.39	0.5
10	J	780	MEDIUM POSITIONAL	0.36	0.5
11	K	780	MEDIUM POSITIONAL	0.41	0.5
12	L	780	MEDIUM POSITIONAL	0.37	0.5
13	M	780	MEDIUM POSITIONAL	0.51	0.5
14	N	780	MEDIUM POSITIONAL	0.48	0.5
15	O	780	MEDIUM POSITIONAL	0.44	0.5
16	P	780	MEDIUM POSITIONAL	0.62	0.5
1	A	908	TIGHT THERMAL	0.12	0.5
2	B	908	TIGHT THERMAL	0.09	0.5
3	C	908	TIGHT THERMAL	0.09	0.5
4	D	908	TIGHT THERMAL	0.07	0.5
5	E	908	TIGHT THERMAL	0.09	0.5
6	F	908	TIGHT THERMAL	0.08	0.5
7	G	908	TIGHT THERMAL	0.08	0.5
8	H	908	TIGHT THERMAL	0.07	0.5
9	I	908	TIGHT THERMAL	0.07	0.5
10	J	908	TIGHT THERMAL	0.07	0.5
11	K	908	TIGHT THERMAL	0.08	0.5
12	L	908	TIGHT THERMAL	0.08	0.5
13	M	908	TIGHT THERMAL	0.1	0.5
14	N	908	TIGHT THERMAL	0.11	0.5
15	O	908	TIGHT THERMAL	0.14	0.5
16	P	908	TIGHT THERMAL	0.12	0.5
1	A	780	MEDIUM THERMAL	0.83	2
2	B	780	MEDIUM THERMAL	0.67	2
3	C	780	MEDIUM THERMAL	0.69	2
4	D	780	MEDIUM THERMAL	0.65	2
5	E	780	MEDIUM THERMAL	0.69	2
6	F	780	MEDIUM THERMAL	0.61	2
7	G	780	MEDIUM THERMAL	0.55	2
8	H	780	MEDIUM THERMAL	0.6	2
9	I	780	MEDIUM THERMAL	0.66	2
10	J	780	MEDIUM THERMAL	0.59	2
11	K	780	MEDIUM THERMAL	0.65	2
12	L	780	MEDIUM THERMAL	0.58	2
13	M	780	MEDIUM THERMAL	0.73	2
14	N	780	MEDIUM THERMAL	0.71	2
15	O	780	MEDIUM THERMAL	0.89	2
16	P	780	MEDIUM THERMAL	0.79	2

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.429	410	-
R_work	0.372	7736	-
all	-	8146	-
obs	-	-	98.87 %

-
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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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