PDB-4wl2: Structure of penicillin V acylase from Pectobacterium atrosepticum

ID or keywords:

Entry

Database: PDB / ID: 4wl2

Title

Structure of penicillin V acylase from Pectobacterium atrosepticum

Components

Putative exported choloylglycine hydrolase

Keywords

HYDROLASE / Ntn hydrolase / choloylglycine / penicillin V / periplasmic

Function / homology

Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / hydrolase activity / Alpha Beta / Putative exported choloylglycine hydrolase

Function and homology information

Biological species

Pectobacterium atrosepticum SCRI1043 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Ramasamy, S. / Avinash, V.S. / Pundle, A.V. / Suresh, C.G.

Citation

Journal: J.Struct.Biol. / Year: 2016
Title: Structural analysis of a penicillin V acylase from Pectobacterium atrosepticum confirms the importance of two Trp residues for activity and specificity
Authors: Avinash, V.S. / Panigrahi, P. / Chand, D. / Pundle, A. / Suresh, C.G. / Ramasamy, S.

History

Deposition	Oct 6, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 7, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 20, 2016	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4wl2.cif.gz	523.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4wl2_validation.pdf.gz	496.3 KB	Display	wwPDB validaton report
Full document	4wl2_full_validation.pdf.gz	549.3 KB	Display
Data in XML	4wl2_validation.xml.gz	94.4 KB	Display
Data in CIF	4wl2_validation.cif.gz	125.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wl/4wl2 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/4wl2	HTTPS FTP

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Related structure data

Similar structure data	6jhf-d 1nhw-d 3f3s-d 2nq8-d 3psd-d 1nhg-d 6p5m-2 2foi-d 1rft-1 1h3g-1 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#166 - Oct 2013 Proteasome similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #176 - Aug 2014 Dynein similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: Putative exported choloylglycine hydrolase

B: Putative exported choloylglycine hydrolase

C: Putative exported choloylglycine hydrolase

D: Putative exported choloylglycine hydrolase

E: Putative exported choloylglycine hydrolase

F: Putative exported choloylglycine hydrolase

G: Putative exported choloylglycine hydrolase

H: Putative exported choloylglycine hydrolase

316 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative exported choloylglycine hydrolase

H: Putative exported choloylglycine hydrolase

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

2

B: Putative exported choloylglycine hydrolase

C: Putative exported choloylglycine hydrolase

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

3

D: Putative exported choloylglycine hydrolase

G: Putative exported choloylglycine hydrolase

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

4

E: Putative exported choloylglycine hydrolase

F: Putative exported choloylglycine hydrolase

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

Unit cell

Length a, b, c (Å)	118.447, 150.206, 185.630
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	1 - 347
2	1	B	1 - 347
1	2	A	1 - 347
2	2	C	1 - 347
1	3	A	1 - 347
2	3	D	1 - 347
1	4	A	1 - 347
2	4	E	1 - 347
1	5	A	1 - 347
2	5	F	1 - 347
1	6	A	1 - 347
2	6	G	1 - 347
1	7	A	1 - 347
2	7	H	1 - 347
1	8	B	1 - 347
2	8	C	1 - 347
1	9	B	1 - 347
2	9	D	1 - 347
1	10	B	1 - 347
2	10	E	1 - 347
1	11	B	1 - 347
2	11	F	1 - 347
1	12	B	1 - 347
2	12	G	1 - 347
1	13	B	1 - 347
2	13	H	1 - 347
1	14	C	1 - 347
2	14	D	1 - 347
1	15	C	1 - 347
2	15	E	1 - 347
1	16	C	1 - 347
2	16	F	1 - 347
1	17	C	1 - 347
2	17	G	1 - 347
1	18	C	1 - 347
2	18	H	1 - 347
1	19	D	1 - 347
2	19	E	1 - 347
1	20	D	1 - 347
2	20	F	1 - 347
1	21	D	1 - 347
2	21	G	1 - 347
1	22	D	1 - 347
2	22	H	1 - 347
1	23	E	1 - 347
2	23	F	1 - 347
1	24	E	1 - 347
2	24	G	1 - 347
1	25	E	1 - 347
2	25	H	1 - 347
1	26	F	1 - 347
2	26	G	1 - 347
1	27	F	1 - 347
2	27	H	1 - 347
1	28	G	1 - 347
2	28	H	1 - 347

NCS ensembles :

#1: Protein	Putative exported choloylglycine hydrolase / PaPVA Mass: 39475.289 Da / Num. of mol.: 8 / Fragment: UNP residues 30-376 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium atrosepticum SCRI1043 (bacteria) Gene: ECA3205 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: Q6D291, penicillin amidase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Putative exported choloylglycine hydrolase / PaPVA

Mass: 39475.289 Da / Num. of mol.: 8 / Fragment: UNP residues 30-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pectobacterium atrosepticum SCRI1043 (bacteria)
Gene: ECA3205 / Plasmid: pET28b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: Q6D291, penicillin amidase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.33 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 14% PEG 3350, 0.2 M sodium potassium tartrate, 0.1 M HEPES pH 7.5 PH range: 7.0-7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 1.435 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 17, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.435 Å / Relative weight: 1
Reflection	Resolution: 2.5→65.7 Å / Num. obs: 101210 / % possible obs: 88.5 % / Observed criterion σ(F): 488 / Redundancy: 7.26 % / R_merge(I) obs: 0.117 / R_sym value: 0.117 / Net I/av σ(I): 5.6 / Net I/σ(I): 11.7
Reflection shell	Resolution: 2.5→2.64 Å / Redundancy: 4.99 % / R_merge(I) obs: 0.786 / Mean I/σ(I) obs: 1.8 / % possible all: 58.2

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
PHASER		phasing
MOSFLM		data processing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→63.43 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.911 / SU B: 10.152 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.896 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24839	5077	5 %	RANDOM
R_work	0.2183	-	-	-
obs	0.21981	96055	88.03 %	-

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: 42.294 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.37 Å²	0 Å²	-0 Å²
2-	-	-0.64 Å²	-0 Å²
3-	-	-	0.27 Å²

Refinement step

Cycle: 1 / Resolution: 2.5→63.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21688	0	0	46	21734

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	22256
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	20816
X-RAY DIFFRACTION	r_angle_refined_deg	1.721	1.943	30240
X-RAY DIFFRACTION	r_angle_other_deg	1.555	3	47976
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.812	5	2768
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.871	24.56	1000
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.286	15	3616
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.796	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	3264
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	25480
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	5208
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	3.662	4.095	11096
X-RAY DIFFRACTION	r_mcbond_other	3.661	4.094	11095
X-RAY DIFFRACTION	r_mcangle_it	5.912	6.136	13856
X-RAY DIFFRACTION	r_mcangle_other	5.911	6.137	13857
X-RAY DIFFRACTION	r_scbond_it	3.445	4.274	11160
X-RAY DIFFRACTION	r_scbond_other	3.445	4.274	11161
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.523	6.271	16385
X-RAY DIFFRACTION	r_long_range_B_refined	9.003	31.69	24735
X-RAY DIFFRACTION	r_long_range_B_other	9.004	31.694	24734
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	20341	0.1
1	2	B	20341	0.1
2	1	A	20270	0.11
2	2	C	20270	0.11
3	1	A	20385	0.11
3	2	D	20385	0.11
4	1	A	20143	0.11
4	2	E	20143	0.11
5	1	A	20306	0.11
5	2	F	20306	0.11
6	1	A	20362	0.1
6	2	G	20362	0.1
7	1	A	20066	0.11
7	2	H	20066	0.11
8	1	B	20406	0.1
8	2	C	20406	0.1
9	1	B	20647	0.09
9	2	D	20647	0.09
10	1	B	20601	0.1
10	2	E	20601	0.1
11	1	B	20480	0.1
11	2	F	20480	0.1
12	1	B	20726	0.09
12	2	G	20726	0.09
13	1	B	20356	0.11
13	2	H	20356	0.11
14	1	C	20655	0.1
14	2	D	20655	0.1
15	1	C	20393	0.1
15	2	E	20393	0.1
16	1	C	20539	0.1
16	2	F	20539	0.1
17	1	C	20591	0.1
17	2	G	20591	0.1
18	1	C	20322	0.11
18	2	H	20322	0.11
19	1	D	20497	0.1
19	2	E	20497	0.1
20	1	D	20389	0.1
20	2	F	20389	0.1
21	1	D	20594	0.09
21	2	G	20594	0.09
22	1	D	20332	0.11
22	2	H	20332	0.11
23	1	E	20415	0.11
23	2	F	20415	0.11
24	1	E	20441	0.11
24	2	G	20441	0.11
25	1	E	20216	0.11
25	2	H	20216	0.11
26	1	F	20769	0.09
26	2	G	20769	0.09
27	1	F	20228	0.11
27	2	H	20228	0.11
28	1	G	20344	0.11
28	2	H	20344	0.11

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.37	305	-
R_work	0.33	5386	-
obs	-	-	67.57 %

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