PDB-2yfk: Crystal structure of a putative transcarbamoylase from Enterococc...

ID or keywords:

Entry

Database: PDB / ID: 2yfk

Title

Crystal structure of a putative transcarbamoylase from Enterococcus faecalis

Components

ASPARTATE/ORNITHINE CARBAMOYLTRANSFERASE

Keywords

TRANSFERASE / TRANSCARBAMYLASE

Function / homology

Aspartate/ornithine carbamoyltransferase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :

Function and homology information

Biological species

ENTEROCOCCUS FAECALIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Polo, L.M. / Fita, I. / Rubio, V.

Citation

Journal: To be Published
Title: Crystal Structure of a Putative Transcarbamoylase from Enterococcus Faecalis with Carbamoyl Phosphate
Authors: Polo, L.M. / Rubio, V.

History

Deposition	Apr 6, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 2, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2yfk.cif.gz	304.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2yfk.ent.gz	250.1 KB	Display	PDB format
PDBx/mmJSON format	2yfk.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/yf/2yfk ftp://data.pdbj.org/pub/pdb/validation_reports/yf/2yfk	HTTPS FTP

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Related structure data

Related structure data	1pvvS 2yff PDB Unreleased entry 2yfm PDB Unreleased entry S: Starting model for refinement
Similar structure data	6bav-d 4r6l-d 7ahk-1 2yxo-1 4s21-d 5e9s-d 6x17-d 1pvw-3 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ASPARTATE/ORNITHINE CARBAMOYLTRANSFERASE

B: ASPARTATE/ORNITHINE CARBAMOYLTRANSFERASE

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

1

A: ASPARTATE/ORNITHINE CARBAMOYLTRANSFERASE

defined by author&software
142 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ASPARTATE/ORNITHINE CARBAMOYLTRANSFERASE

defined by software
142 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	117.368, 117.368, 120.232
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B
1	4	A
2	4	B
1	5	A
2	5	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	1 - 286
2	1	1	4	B	1 - 286
1	1	2	5	A	287 - 291
2	1	2	5	B	287 - 291
1	1	3	4	A	292 - 362
2	1	3	4	B	292 - 362
1	1	4	4	A	363 - 364
2	1	4	4	B	363 - 364
1	1	5	4	A	365 - 450
2	1	5	4	B	365 - 450

NCS ensembles :

ID
1
2
3
4
5

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.50588, 0.86244, 0.01674), (0.86248, 0.50604, -0.00741), (-0.01486, 0.01069, -0.99983)	-58.62421, 33.96548, -12.73859
3	given	(-0.508682, 0.860863, -0.012543), (0.860824, 0.508805, 0.010007), (0.014997, -0.005707, -0.999871)	-59.12847, 33.32657, -11.62774
4	given	(-0.493327, 0.868477, -0.048745), (0.869828, 0.492207, -0.033627), (-0.005211, -0.058989, -0.998245)	-58.32052, 36.01291, -11.01038
5	given	(-0.492071, 0.870339, -0.019406), (0.870299, 0.492344, 0.013261), (0.021095, -0.010364, -0.999724)	-59.05326, 34.59476, -11.19205
6	given	(-0.521798, 0.852768, -0.022666), (0.85126, 0.522237, 0.051241), (0.055534, 0.007443, -0.998429)	-59.2342, 32.51113, -10.57013
7	given	(-0.506254, 0.862384, -0.000552), (0.862355, 0.506242, 0.007985), (0.007165, 0.003566, -0.999968)	-58.98514, 33.47118, -12.23438

#1: Protein	ASPARTATE/ORNITHINE CARBAMOYLTRANSFERASE Mass: 47261.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Strain: SD10 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: C7YCV8, Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.82 Å³/Da / Density % sol: 56.03 % Description: THE METHIONINE RESIDUES WERE ASIGNED TO THE SEQUENCE USING THE ANOMALOUS SIGNAL FROM ANOTHER CRYSTAL CONTAINING SEMET AT LOW RESOLUTION.
Crystal grow	pH: 8 Details: LITHIUM SULFATE 180MM, PEG3350 24%, HEPES NA PH8 100MM, TRIS HCL PH7.5 40MM

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-2 / Wavelength: 0.933

Detector

Type: ADSC CCD / Detector: CCD / Date: Jun 18, 2007

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.933 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.551
1	1	K, H, -L	2	0.449

Reflection

Resolution: 2.55→30 Å / Num. obs: 30659 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / B_iso Wilson estimate: 53 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 8.1

Reflection shell

Resolution: 2.55→2.69 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.24 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0112	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PVV

1pvv

Resolution: 2.55→30 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.923 / SU B: 18.503 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20162	1544	5 %	RANDOM
R_work	0.16925	-	-	-
obs	0.17083	29091	99.83 %	-

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 mean: 35.224 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.99 Å²	0 Å²	0 Å²
2-	-	-6.99 Å²	0 Å²
3-	-	-	13.97 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5993	0	0	63	6056

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	6112
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4064
X-RAY DIFFRACTION	r_angle_refined_deg	0.913	1.964	8265
X-RAY DIFFRACTION	r_angle_other_deg	0.798	3	9967
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.662	5	766
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.512	25.376	279
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.177	15	1065
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.369	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	920
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	6823
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1179
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	3527	medium positional	0.26	0.5
1	2	B	3527	medium positional	0.26	0.5
2	1	A	29	medium positional	0.13	0.5
2	2	B	29	medium positional	0.13	0.5
3	1	A	928	medium positional	0.19	0.5
3	2	B	928	medium positional	0.19	0.5
4	1	A	39	medium positional	0.37	0.5
4	2	B	39	medium positional	0.37	0.5
5	1	A	423	medium positional	0.25	0.5
5	2	B	423	medium positional	0.25	0.5
2	1	A	24	loose positional	0.41	5
2	2	B	24	loose positional	0.41	5
1	1	A	3527	medium thermal	1.06	2
1	2	B	3527	medium thermal	1.06	2
2	1	A	29	medium thermal	4.32	2
2	2	B	29	medium thermal	4.32	2
3	1	A	928	medium thermal	0.89	2
3	2	B	928	medium thermal	0.89	2
4	1	A	39	medium thermal	1.07	2
4	2	B	39	medium thermal	1.07	2
5	1	A	423	medium thermal	0.53	2
5	2	B	423	medium thermal	0.53	2
2	1	A	24	loose thermal	4.48	10
2	2	B	24	loose thermal	4.48	10

LS refinement shell

Resolution: 2.549→2.614 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.409	112	-
R_work	0.323	2074	-
obs	-	-	98.11 %

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	2.4444	0.0105	2.1318	3.1734	-0.1532	5.2477	-0.2342	-0.0569	0.5132	0.2756	-0.004	0.1674	-0.2348	0.2646	0.2382	0.162	0.0121	0.0602	0.1296	-0.0295	0.2356	-7.9822	26.4255	2.1069
2	1.8625	0.0742	0.7161	3.5871	0.4902	1.3111	-0.0461	0.2029	0.1958	-0.1914	-0.0046	0.0144	-0.0255	0.1879	0.0506	0.1087	0.0024	0.0408	0.1353	-0.0027	0.0762	-1.0347	15.9995	-1.9324
3	15.2655	-3.1791	1.1684	7.9524	-0.9927	1.8171	0.1915	0.8891	0.0316	-0.7067	-0.2177	0.0758	-0.7157	0.5549	0.0262	0.452	-0.2123	-0.0405	0.2198	-0.0567	0.172	0.522	10.5849	-7.6202
4	1.3266	1.6746	-0.1192	2.8296	-0.4243	0.301	-0.1222	0.2737	0.0452	-0.3661	0.1654	0.1128	0.0192	-0.0926	-0.0432	0.1823	0.0394	-0.0148	0.2271	-0.0094	0.1951	-13.2302	13.5664	-12.6613
5	2.5362	0.9512	0.6265	0.8902	0.1371	2.0645	-0.0191	0.1269	0.1858	-0.2065	0.0386	0.2019	0.0059	-0.1547	-0.0195	0.2116	0.0194	-0.0185	0.1571	0.0504	0.2489	-0.5278	36.1607	-18.9855
6	6.8461	4.0009	1.9546	2.4359	1.35	1.9198	-0.0753	0.673	-0.4481	0.0713	0.2807	-0.1429	0.1634	-0.1459	-0.2054	0.4763	-0.0089	0.0393	0.4524	0.0124	0.5103	-5.2651	24.2818	-38.8356
7	1.0015	0.2465	0.0067	1.514	-0.7598	1.5617	-0.0152	0.0338	0.0606	-0.1101	-0.0397	-0.1383	0.1031	0.2185	0.0549	0.1195	-0.0064	-0.0022	0.0886	-0.0338	0.2071	8.4434	25.0434	-10.7571
8	3.726	-0.0636	1.0782	2.3565	-0.4313	2.1663	-0.0716	0.3929	0.0518	-0.1573	-0.0809	-0.5859	-0.0466	0.221	0.1524	0.1108	-0.0226	0.0731	0.1547	-0.009	0.2478	-31.3935	40.6468	-14.1891
9	2.4011	0.6911	-0.3921	2.4515	-0.1534	0.0726	-0.0675	-0.1288	-0.0155	0.2471	0.0856	-0.1424	-0.0194	-0.0007	-0.0181	0.2258	0.0113	0.004	0.145	0.0244	0.1237	-46.3256	40.9965	-10.3582
10	12.3871	-1.928	0.6413	11.1359	-0.4849	0.0472	-0.1979	-0.6172	0.1564	0.9989	0.2079	0.0983	-0.0482	-0.0368	-0.01	0.1333	0.0192	0.0758	0.1183	0.044	0.1379	-49.8406	39.765	-4.8961
11	0.8043	1.2648	0.2021	2.8304	0.7722	0.3016	0.0695	-0.1907	-0.0826	0.3898	-0.0914	-0.1096	0.1737	0.0568	0.0218	0.1756	0.0112	-0.0064	0.1751	0.0237	0.2079	-40.3513	29.4779	0.2443
12	0.4953	-0.6413	0.2311	2.7915	-0.7171	2.6905	0.0711	-0.2183	-0.0614	0.1076	-0.079	-0.238	0.0797	0.2368	0.0079	0.1303	-0.0159	-0.0556	0.2498	-0.0113	0.2517	-27.4197	51.8807	6.5856
13	0.9557	-2.1179	-0.019	6.2108	-1.2499	1.2039	0.0016	-0.0813	-0.0918	-0.0226	0.0489	0.1685	-0.1082	-0.0709	-0.0505	0.439	0.0267	-0.0452	0.4462	0.0711	0.4099	-36.053	41.7265	26.102
14	0.7246	0.5903	0.4594	1.838	0.3759	1.0638	-0.0477	-0.0538	0.1361	0.0333	-0.0166	0.0408	-0.1647	-0.0392	0.0643	0.0761	0.0128	0.0199	0.1628	0.0101	0.2035	-41.5325	53.9225	-1.9408

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 32
2	X-RAY DIFFRACTION	2	A	33 - 73
3	X-RAY DIFFRACTION	3	A	74 - 86
4	X-RAY DIFFRACTION	4	A	87 - 175
5	X-RAY DIFFRACTION	5	A	176 - 280
6	X-RAY DIFFRACTION	6	A	281 - 307
7	X-RAY DIFFRACTION	7	A	308 - 397
8	X-RAY DIFFRACTION	8	B	2 - 36
9	X-RAY DIFFRACTION	9	B	37 - 73
10	X-RAY DIFFRACTION	10	B	74 - 86
11	X-RAY DIFFRACTION	11	B	87 - 175
12	X-RAY DIFFRACTION	12	B	176 - 280
13	X-RAY DIFFRACTION	13	B	281 - 307
14	X-RAY DIFFRACTION	14	B	308 - 397

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