PDB-4iqe: Crystal Structure of Carboxyvinyl-Carboxyphosphonate Phosphorylmu...

ID or keywords:

Entry

Database: PDB / ID: 4iqe

Title

Crystal Structure of Carboxyvinyl-Carboxyphosphonate Phosphorylmutase from Bacillus anthracis str. Ames Ancestor

Components

Carboxyvinyl-carboxyphosphonate phosphorylmutase

Keywords

LYASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel

Function / homology

Function and homology information

methylisocitrate lyase / propionate catabolic process, 2-methylcitrate cycle / methylisocitrate lyase activity / metal ion binding
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.501 Å

Authors

Kim, Y. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Crystal Structure of Carboxyvinyl-Carboxyphosphonate Phosphorylmutase from Bacillus anthracis str. Ames Ancestor
Authors: Kim, Y. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jan 11, 2013	Deposition site: RCSB / Processing site: RCSB
Supersession	Jan 23, 2013	ID: 3KZ2
Revision 1.0	Jan 23, 2013	Provider: repository / Type: Initial release
Revision 1.1	Dec 3, 2014	Group: Structure summary
Revision 1.2	Jan 24, 2018	Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_atoms / Item: _audit_author.name
Revision 1.3	Sep 20, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4iqe.cif.gz	235.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4iqe.ent.gz	191.8 KB	Display	PDB format
PDBx/mmJSON format	4iqe.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4iqe_validation.pdf.gz	435.5 KB	Display	wwPDB validaton report
Full document	4iqe_full_validation.pdf.gz	440.7 KB	Display
Data in XML	4iqe_validation.xml.gz	22.4 KB	Display
Data in CIF	4iqe_validation.cif.gz	31.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iq/4iqe ftp://data.pdbj.org/pub/pdb/validation_reports/iq/4iqe	HTTPS FTP

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Related structure data

Related structure data	3ih1 PDB Unreleased entryS 4iqd S: Starting model for refinement
Similar structure data	4iqd-d 6gwy-1 3ioh-1 1ep3-d 5c36-1 6nkf-1 4kc2-1 6syl-d 3mwt-3 2okg-2 Search similar-shape structures by Omokage search (details) 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: IDP02080

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (2)

Deposited unit

A: Carboxyvinyl-carboxyphosphonate phosphorylmutase

B: Carboxyvinyl-carboxyphosphonate phosphorylmutase

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

1

Idetical with deposited unit
defined by author&software

2

A: Carboxyvinyl-carboxyphosphonate phosphorylmutase

B: Carboxyvinyl-carboxyphosphonate phosphorylmutase

A: Carboxyvinyl-carboxyphosphonate phosphorylmutase

B: Carboxyvinyl-carboxyphosphonate phosphorylmutase

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

Unit cell

Length a, b, c (Å)	106.166, 106.166, 113.449
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Details

dimer as in the asymmetric unit

#1: Protein	Carboxyvinyl-carboxyphosphonate phosphorylmutase / Methylisocitrate lyase Mass: 33648.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: prpB, yqiQ / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic References: UniProt: Q81QR8, UniProt: A0A6L7HJ56*PLUS, methylisocitrate lyase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Carboxyvinyl-carboxyphosphonate phosphorylmutase / Methylisocitrate lyase

Mass: 33648.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: prpB, yqiQ / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q81QR8, UniProt: A0A6L7HJ56*PLUS, methylisocitrate lyase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.74 Å³/Da / Density % sol: 55.15 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 5 % Tecsimate pH 7.0, 0.1 M Hepes pH 7.0, 10 % PEG 5000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97951 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2009 / Details: mirrors
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97951 Å / Relative weight: 1
Reflection twin	Operator: -h,-k,l / Fraction: 0.49
Reflection	Resolution: 2.5→48.08 Å / Num. all: 26004 / Num. obs: 26004 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / B_iso Wilson estimate: 50.4 Å² / R_sym value: 0.119 / Net I/σ(I): 10.2
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 3.44 / Num. unique all: 1292 / R_sym value: 0.759 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		data collection
HKL-3000		phasing
MOLREP		phasing
PHENIX	(phenix.refine: 1.8.1_1161)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ID 3IH1

3ih1
PDB Unreleased entry

Resolution: 2.501→48.08 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.43 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.178	1316	5.09 %	random
R_work	0.159	-	-	-
obs	0.163	25870	99.51 %	-
all	-	25870	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.501→48.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4421	0	0	147	4568

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4489
X-RAY DIFFRACTION	f_angle_d	0.574	6081
X-RAY DIFFRACTION	f_dihedral_angle_d	14.562	1655
X-RAY DIFFRACTION	f_chiral_restr	0.041	718
X-RAY DIFFRACTION	f_plane_restr	0.002	794

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
2.5015-2.6017	0.3213	139	0.2529	2656	2795	94
2.6017-2.72	0.2691	131	0.2451	2681	2812	94
2.72-2.8634	0.2548	151	0.2179	2686	2837	94
2.8634-3.0427	0.2479	145	0.2001	2706	2851	94
3.0427-3.2775	0.2062	130	0.178	2712	2842	95
3.2775-3.607	0.162	143	0.1508	2738	2881	95
3.607-4.1282	0.1415	165	0.1328	2709	2874	94
4.1282-5.1984	0.1282	152	0.1233	2773	2925	95
5.1984-34.977	0.1618	152	0.1566	2892	3044	95

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	3.6326	0.4896	2.4786	2.6726	0.7623	5.0422	0.225	0.2999	-0.6139	0.3931	-0.1569	0.4964	0.5622	-0.0959	-0.0812	0.3463	0.0534	0.0022	0.2763	-0.0413	0.6008	47.8488	-60.4011	40.4142
2	3.1072	-1.3456	-0.6546	1.4262	-0.1259	1.5419	-0.0201	-0.0204	0.0748	-0.1506	0.1632	-0.0702	0.2321	-0.0125	-0.1586	0.3277	-0.0459	-0.001	0.2845	-0.0419	0.2827	45.6146	-43.989	42.8666
3	2.5825	-0.1725	-0.866	2.784	1.3976	7.243	-0.2285	-0.1322	0.2496	-0.009	0.2207	0.0905	0.2168	0.034	-0.0383	0.2497	0.0174	-0.0161	0.2681	-0.0022	0.3593	40.5682	-49.7183	39.9215
4	1.9551	-0.257	-0.8142	0.5115	-0.4361	1.1686	-0.0384	-0.0406	0.0954	-0.0716	0.0612	0.0041	0.1129	-0.3349	-0.0459	0.329	-0.0511	-0.0649	0.319	0.0095	0.3629	35.5232	-48.483	55.4736
5	1.5931	-0.2948	1.205	0.8354	0.5151	2.2106	0.1019	-0.0153	-0.1953	0.081	-0.0199	-0.0377	0.217	-0.2632	-0.0532	0.3098	-0.0137	-0.0012	0.2458	0.0195	0.3575	43.1656	-54.5128	62.6104
6	4.0554	1.8062	0.524	5.5141	1.4115	2.8704	-0.2386	0.1474	-0.1667	0.3552	0.2879	-0.0121	0.0301	0.5631	-0.0054	0.3159	0.0627	-0.0635	0.3279	0.0456	0.3271	57.0732	-48.6548	63.349
7	2.5985	1.5748	-0.2246	4.054	-0.9531	1.821	0.0073	0.3458	-0.0582	0.1454	0.0539	-0.3817	-0.1558	-0.0634	-0.0082	0.329	0.0224	0.0048	0.3159	-0.0348	0.2659	56.7874	-42.944	54.426
8	1.7324	-1.1468	1.1847	2.38	-2.6385	3.3001	0.0107	0.0041	-0.0995	0.2973	0.1004	0.1433	-0.1849	0.0819	-0.1004	0.308	0.024	-0.0048	0.2949	-0.055	0.2697	52.3362	-34.9214	43.6232
9	2.2687	-0.7668	-0.1495	4.2946	-2.5205	1.9759	0.0361	0.2914	-0.1305	-0.3388	-0.0435	0.2851	-0.1079	0.0131	-0.0616	0.2779	0.0038	0.0288	0.3531	-0.0323	0.2549	50.9386	-32.6278	24.3349
10	6.6927	1.6309	0.3318	6.2887	1.7927	6.3122	-0.4503	0.9011	-0.4664	-0.5289	0.5722	-0.0776	0.1266	0.4185	-0.1422	0.3581	0.0064	0.032	0.5931	-0.1741	0.4918	42.8052	-53.2124	14.8728
11	1.1572	0.3928	0.9621	1.4135	0.3897	1.6233	0.0606	-0.0807	0.163	0.032	0.0039	0.1178	0.0188	-0.188	-0.0701	0.2708	0.0071	0.0247	0.3613	0.0461	0.3145	29.7893	-29.7645	29.5217
12	1.6577	-1.0878	-0.1057	3.1175	-0.002	0.8253	-0.0274	0.1953	0.0301	-0.5133	0.2851	0.3033	0.097	0.2674	-0.2383	0.4593	-0.0041	-0.0576	0.5674	0.0105	0.3423	25.5398	-37.4557	11.6907
13	2.8924	0.2831	-1.1686	0.7859	-0.8689	2.0877	-0.0814	0.1143	0.2762	-0.0381	0.0959	0.0806	-0.069	-0.0775	-0.001	0.3406	0.0527	-0.0056	0.3272	0.0418	0.3008	30.5187	-23.569	10.1396
14	0.6345	0.0581	0.7118	0.3675	-0.3089	1.715	0.0025	0.1739	0.0576	0.0459	-0.0467	0.1094	-0.0408	0.0531	0.0703	0.2425	-0.016	0.0532	0.2917	0.0006	0.3262	47.2876	-27.0845	25.2345
15	8.5501	-1.118	-0.591	2.9818	-0.3292	2.7095	0.3534	-0.5444	1.2289	0.1368	-0.0857	-0.0029	0.1157	0.0583	-0.2388	0.3544	-0.095	0.025	0.2992	-0.0879	0.3808	50.7416	-29.8075	47.5127
16	3.8059	-0.3813	-2.0711	4.1972	0.7814	8.4322	0.1467	-0.1505	0.7457	0.3354	-0.3831	0.4869	-0.5347	0.1019	0.2021	0.5171	-0.029	0.0298	0.3592	-0.0556	0.5888	29.6979	-26.0144	60.1736

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 72 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 73 through 92 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 93 through 138 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 139 through 187 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 188 through 207 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 208 through 227 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 228 through 261 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 262 through 281 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 282 through 296 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 8 through 121 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 122 through 153 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 154 through 214 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 215 through 261 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 262 through 282 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 283 through 297 )

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