PDB-2a81: carboxymethylproline synthase (CarB) from pectobacterium carotovo...

ID or keywords:

Entry

Database: PDB / ID: 2a81

Title

carboxymethylproline synthase (CarB) from pectobacterium carotovora, complexed with acetyl CoA and bicine

Components

CarB

Keywords

BIOSYNTHETIC PROTEIN /

carbapenem /

carbapenam /

crotonase /

antibiotic /

beta-lactam /

bicine /

acetyl coenzyme a

Function / homology

Function and homology information

carboxymethylproline synthase / antibiotic biosynthetic process /

transferase activity
Similarity search - Function

Biological species

Pectobacterium carotovorum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.15 Å

Authors

Sleeman, M.C. / Sorensen, J.L. / Batchelar, E.T. / McDonough, M.A. / Schofield, C.J.

Citation

Journal: J.Biol.Chem. / Year: 2005
Title: Structural and Mechanistic Studies on Carboxymethylproline Synthase (CarB), a Unique Member of the Crotonase Superfamily Catalyzing the First Step in Carbapenem Biosynthesis.
Authors: Sleeman, M.C. / Sorensen, J.L. / Batchelar, E.T. / McDonough, M.A. / Schofield, C.J.

History

Deposition	Jul 7, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 23, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Aug 23, 2023	Group: Data collection / Database references ...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 / struct_ncs_dom_lim / struct_site 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.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2a81.cif.gz	274.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a8/2a81 ftp://data.pdbj.org/pub/pdb/validation_reports/a8/2a81	HTTPS FTP

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Related structure data

Related structure data	2a7kSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2a7k-2 2a7k-3 2a7k-1 3l3s-4 5u8o-1 2r8x-5 2z0r-8 4fn7-d 4fnb-1 3r6h-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CarB

B: CarB

C: CarB

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	139.605, 139.605, 78.546
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:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	MET	MET	1	A	A	1	1
2	1	1	MET	MET	MET	MET	1	B	B	1	1
3	1	1	MET	MET	MET	MET	1	C	C	1	1
4	2	1	VAL	VAL	PHE	PHE	5	A	A	2 - 3	2 - 3
5	2	1	VAL	VAL	PHE	PHE	5	B	B	2 - 3	2 - 3
6	2	1	VAL	VAL	PHE	PHE	5	C	C	2 - 3	2 - 3
7	3	1	GLU	GLU	GLU	GLU	1	A	A	4	4
8	3	1	GLU	GLU	GLU	GLU	1	B	B	4	4
9	3	1	GLU	GLU	GLU	GLU	1	C	C	4	4
10	4	1	GLU	GLU	GLU	GLU	5	A	A	5	5
11	4	1	GLU	GLU	GLU	GLU	5	B	B	5	5
12	4	1	GLU	GLU	GLU	GLU	5	C	C	5	5
13	5	1	ASN	ASN	LEU	LEU	1	A	A	6 - 15	6 - 15
14	5	1	ASN	ASN	LEU	LEU	1	B	B	6 - 15	6 - 15
15	5	1	ASN	ASN	LEU	LEU	1	C	C	6 - 15	6 - 15
16	6	1	ASP	ASP	ASP	ASP	5	A	A	16	16
17	6	1	ASP	ASP	ASP	ASP	5	B	B	16	16
18	6	1	ASP	ASP	ASP	ASP	5	C	C	16	16
19	7	1	HIS	HIS	ASN	ASN	1	A	A	17 - 19	17 - 19
20	7	1	HIS	HIS	ASN	ASN	1	B	B	17 - 19	17 - 19
21	7	1	HIS	HIS	ASN	ASN	1	C	C	17 - 19	17 - 19
22	8	1	LYS	LYS	LYS	LYS	5	A	A	20	20
23	8	1	LYS	LYS	LYS	LYS	5	B	B	20	20
24	8	1	LYS	LYS	LYS	LYS	5	C	C	20	20
25	9	1	HIS	HIS	SER	SER	1	A	A	21 - 25	21 - 25
26	9	1	HIS	HIS	SER	SER	1	B	B	21 - 25	21 - 25
27	9	1	HIS	HIS	SER	SER	1	C	C	21 - 25	21 - 25
28	10	1	ARG	ARG	ARG	ARG	5	A	A	26	26
29	10	1	ARG	ARG	ARG	ARG	5	B	B	26	26
30	10	1	ARG	ARG	ARG	ARG	5	C	C	26	26
31	11	1	THR	THR	LEU	LEU	1	A	A	27 - 28	27 - 28
32	11	1	THR	THR	LEU	LEU	1	B	B	27 - 28	27 - 28
33	11	1	THR	THR	LEU	LEU	1	C	C	27 - 28	27 - 28
34	12	1	GLU	GLU	GLU	GLU	4	A	A	29	29
35	12	1	GLU	GLU	GLU	GLU	4	B	B	29	29
36	12	1	GLU	GLU	GLU	GLU	4	C	C	29	29
37	13	1	THR	THR	ASP	ASP	1	A	A	30 - 42	30 - 42
38	13	1	THR	THR	ASP	ASP	1	B	B	30 - 42	30 - 42
39	13	1	THR	THR	ASP	ASP	1	C	C	30 - 42	30 - 42
40	14	1	ASP	ASP	ASP	ASP	6	A	A	43	43
41	14	1	ASP	ASP	ASP	ASP	6	B	B	43	43
42	14	1	ASP	ASP	ASP	ASP	6	C	C	43	43
43	15	1	SER	SER	VAL	VAL	1	A	A	44 - 45	44 - 45
44	15	1	SER	SER	VAL	VAL	1	B	B	44 - 45	44 - 45
45	15	1	SER	SER	VAL	VAL	1	C	C	44 - 45	44 - 45
46	16	1	ARG	ARG	PHE	PHE	4	A	A	56 - 58	56 - 58
47	16	1	ARG	ARG	PHE	PHE	4	B	B	56 - 58	56 - 58
48	16	1	ARG	ARG	PHE	PHE	4	C	C	56 - 58	56 - 58
49	17	1	ARG	ARG	ILE	ILE	6	A	A	72 - 80	72 - 80
50	17	1	ARG	ARG	ILE	ILE	6	B	B	72 - 80	72 - 80
51	17	1	ARG	ARG	ILE	ILE	6	C	C	72 - 80	72 - 80
52	18	1	ASP	ASP	ALA	ALA	1	A	A	81 - 105	81 - 105
53	18	1	ASP	ASP	ALA	ALA	1	B	B	81 - 105	81 - 105
54	18	1	ASP	ASP	ALA	ALA	1	C	C	81 - 105	81 - 105
55	19	1	ILE	ILE	MET	MET	4	A	A	106 - 108	106 - 108
56	19	1	ILE	ILE	MET	MET	4	B	B	106 - 108	106 - 108
57	19	1	ILE	ILE	MET	MET	4	C	C	106 - 108	106 - 108
58	20	1	GLY	GLY	MET	MET	1	A	A	109 - 129	109 - 129
59	20	1	GLY	GLY	MET	MET	1	B	B	109 - 129	109 - 129
60	20	1	GLY	GLY	MET	MET	1	C	C	109 - 129	109 - 129
61	21	1	PRO	PRO	ALA	ALA	4	A	A	130 - 142	130 - 142
62	21	1	PRO	PRO	ALA	ALA	4	B	B	130 - 142	130 - 142
63	21	1	PRO	PRO	ALA	ALA	4	C	C	130 - 142	130 - 142
64	22	1	ALA	ALA	ILE	ILE	1	A	A	143 - 157	143 - 157
65	22	1	ALA	ALA	ILE	ILE	1	B	B	143 - 157	143 - 157
66	22	1	ALA	ALA	ILE	ILE	1	C	C	143 - 157	143 - 157
67	23	1	ILE	ILE	ILE	ILE	2	A	A	158	158
68	23	1	ILE	ILE	ILE	ILE	2	B	B	158	158
69	23	1	ILE	ILE	ILE	ILE	2	C	C	158	158
70	24	1	TYR	TYR	GLN	GLN	1	A	A	159 - 162	159 - 162
71	24	1	TYR	TYR	GLN	GLN	1	B	B	159 - 162	159 - 162
72	24	1	TYR	TYR	GLN	GLN	1	C	C	159 - 162	159 - 162
73	25	1	SER	SER	ASP	ASP	4	A	A	163 - 165	163 - 165
74	25	1	SER	SER	ASP	ASP	4	B	B	163 - 165	163 - 165
75	25	1	SER	SER	ASP	ASP	4	C	C	163 - 165	163 - 165
76	26	1	ALA	ALA	SER	SER	1	A	A	166 - 197	166 - 197
77	26	1	ALA	ALA	SER	SER	1	B	B	166 - 197	166 - 197
78	26	1	ALA	ALA	SER	SER	1	C	C	166 - 197	166 - 197
79	27	1	TYR	TYR	ILE	ILE	4	A	A	198 - 204	198 - 204
80	27	1	TYR	TYR	ILE	ILE	4	B	B	198 - 204	198 - 204
81	27	1	TYR	TYR	ILE	ILE	4	C	C	198 - 204	198 - 204
82	28	1	ASN	ASN	ILE	ILE	1	A	A	205 - 215	205 - 215
83	28	1	ASN	ASN	ILE	ILE	1	B	B	205 - 215	205 - 215
84	28	1	ASN	ASN	ILE	ILE	1	C	C	205 - 215	205 - 215
85	29	1	HIS	HIS	HIS	HIS	3	A	A	216	216
86	29	1	HIS	HIS	HIS	HIS	3	B	B	216	216
87	29	1	HIS	HIS	HIS	HIS	3	C	C	216	216
88	30	1	LEU	LEU	SER	SER	5	A	A	217 - 225	217 - 225
89	30	1	LEU	LEU	SER	SER	5	B	B	217 - 225	217 - 225
90	30	1	LEU	LEU	SER	SER	5	C	C	217 - 225	217 - 225
91	31	1	ARG	ARG	ARG	ARG	3	A	A	46	46
92	31	1	ARG	ARG	ARG	ARG	3	B	B	46	46
93	31	1	ARG	ARG	ARG	ARG	3	C	C	46	46
94	32	1	ALA	ALA	ALA	ALA	1	A	A	47 - 54	47 - 54
95	32	1	ALA	ALA	ALA	ALA	1	B	B	47 - 54	47 - 54
96	32	1	ALA	ALA	ALA	ALA	1	C	C	47 - 54	47 - 54
97	33	1	GLU	GLU	GLU	GLU	5	A	A	55	55
98	33	1	GLU	GLU	GLU	GLU	5	B	B	55	55
99	33	1	GLU	GLU	GLU	GLU	5	C	C	55	55
1	1	2	GLY	GLY	SER	SER	4	B	B	62 - 71	62 - 71
2	1	2	GLY	GLY	SER	SER	4	C	C	62 - 71	62 - 71

NCS ensembles :

ID
1
2

Details

The biological unit is a trimer. There is 1 biological unit in the asymmetric unit (chains A, B & C)

#1: Protein	CarB Mass: 27608.275 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Gene: CarB / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9XB60
#2: Chemical	ChemComp-ACO / ACETYL COENZYME A / Acetyl-CoA Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula*: C₂₃H₃₈N₇O₁₇P₃S
#3: Chemical	ChemComp-BCN / BICINE / Bicine Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄ / Comment: pH buffer*YM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 53.6 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 6000, BICINE, pH 8, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SRS

/ Beamline: PX10.1 / Wavelength: 1.009 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2005 / Details: mirrors

Radiation

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

Radiation wavelength

Wavelength: 1.009 Å / Relative weight: 1

Reflection

Resolution: 3.15→47.91 Å / Num. obs: 15149 / % possible obs: 99.3 % / Redundancy: 5.9 % / R_merge(I) obs: 0.203 / Χ²: 1.012

Reflection shell

Resolution (Å)	% possible obs (%)	Redundancy (%)	R_merge(I) obs	Num. measured obs	Χ²	Diffraction-ID
3.15-3.26	94.3	3.9	0.562	1432	0.994	1
3.26-3.39	99.1	5.2	0.473	1490	0.999	1
3.39-3.55	99.7	5.9	0.432	1504	1.056	1
3.55-3.73	99.9	6.2	0.321	1521	1.043	1
3.73-3.97	100	6.2	0.261	1525	1.054	1
3.97-4.27	100	6.2	0.177	1498	1.015	1
4.27-4.7	100	6.2	0.149	1531	1.037	1
4.7-5.38	100	6.2	0.15	1532	1.004	1
5.38-6.78	100	6.2	0.179	1533	0.954	1
6.78-50	99.7	6	0.062	1583	0.952	1

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Phasing

Phasing MR

	Highest resolution	Lowest resolution
Translation	3.05 Å	47.669 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
REFMAC	5.2.0005	refinement
PDB_EXTRACT	1.7	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: monomer of 2A7K

2a7k

Resolution: 3.15→47.91 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.883 / SU B: 44.072 / SU ML: 0.323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.232	798	5.3 %	RANDOM
R_work	0.192	-	-	-
all	0.194	-	-	-
obs	0.194	15136	99.23 %	-

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: 45.538 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.75 Å²	0.38 Å²	0 Å²
2-	-	0.75 Å²	0 Å²
3-	-	-	-1.13 Å²

Refinement step

Cycle: LAST / Resolution: 3.15→47.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5304	0	52	0	5356

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	5456
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4913
X-RAY DIFFRACTION	r_angle_refined_deg	1.114	1.947	7407
X-RAY DIFFRACTION	r_angle_other_deg	0.747	3.001	11321
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.498	5	694
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.448	24.274	248
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.913	15	865
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.216	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	850
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	6163
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1111
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	1201
X-RAY DIFFRACTION	r_nbd_other	0.17	0.2	4969
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	2735
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	3209
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	102
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.256	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.216	0.2	42
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.285	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	0.182	1.5	3553
X-RAY DIFFRACTION	r_mcbond_other	0.042	1.5	1415
X-RAY DIFFRACTION	r_mcangle_it	0.307	2	5549
X-RAY DIFFRACTION	r_scbond_it	0.505	3	2128
X-RAY DIFFRACTION	r_scangle_it	0.903	4.5	1858

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms	Type	Weight
1	1	A	2250	0.02	TIGHT POSITIONAL	0.05
1	2	B	2250	0.02	TIGHT POSITIONAL	0.05
1	3	C	2250	0.02	TIGHT POSITIONAL	0.05
1	1	A	523	0.44	MEDIUM POSITIONAL	0.5
1	2	B	523	0.34	MEDIUM POSITIONAL	0.5
1	3	C	523	0.47	MEDIUM POSITIONAL	0.5
1	1	A	265	0.96	LOOSE POSITIONAL	5
1	2	B	265	0.76	LOOSE POSITIONAL	5
1	3	C	265	0.85	LOOSE POSITIONAL	5
1	1	A	2250	0.03	TIGHT THERMAL	0.5
1	2	B	2250	0.03	TIGHT THERMAL	0.5
1	3	C	2250	0.03	TIGHT THERMAL	0.5
1	1	A	523	0.28	MEDIUM THERMAL	2
1	2	B	523	0.22	MEDIUM THERMAL	2
1	3	C	523	0.24	MEDIUM THERMAL	2
1	1	A	265	0.95	LOOSE THERMAL	10
1	2	B	265	0.76	LOOSE THERMAL	10
1	3	C	265	0.77	LOOSE THERMAL	10
2	1	B	139	0.31	MEDIUM POSITIONAL	0.5
2	1	B	139	0.19	MEDIUM THERMAL	2

LS refinement shell

Resolution: 3.15→3.232 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.352	52	-
R_work	0.317	983	-
all	-	1035	-
obs	-	-	93.08 %

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	2.303	0.419	0.2142	1.1696	0.2658	2.2421	-0.0548	0.0427	-0.0766	-0.0147	0.075	0.1083	-0.0226	-0.4307	-0.0202	-0.299	-0.0376	-0.0191	-0.0782	0.0343	-0.2128	9.8797	-51.8633	-7.3267
2	2.6663	0.8046	-0.2938	2.1811	-0.8213	2.679	-0.1252	0.2028	0.0986	-0.2841	0.1342	-0.0059	-0.4036	0.1564	-0.009	-0.0837	-0.0984	-0.0391	-0.215	0.0011	-0.2274	38.224	-33.9344	-14.5371
3	0.8715	0.3465	0.2001	2.9444	-0.6399	3.5056	0.0283	-0.0594	-0.062	0.1167	-0.024	-0.2257	-0.1488	0.2738	-0.0044	-0.311	-0.0409	-0.0666	-0.2498	0.0025	-0.1978	34.4701	-48.7681	16.2067

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	1 - 235	1 - 235
2	2	B	B	1 - 231	1 - 231
3	3	C	C	1 - 231	1 - 231

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