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- PDB-7pu6: STRUCTURE OF ESTER-HYDROLASE EH7 FROM THE METAGENOME OF MARINE SE... -

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Basic information

Entry
Database: PDB / ID: 7pu6
TitleSTRUCTURE OF ESTER-HYDROLASE EH7 FROM THE METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY) COMPLEXED WITH A DERIVATIVE OF OCTYL 4-NITROPHENYL HEXYLPHOSPHONATE
ComponentsEsterase
KeywordsHYDROLASE / Ester Hydrolase / Complex
Function / homologyBeta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / hexyl(octoxy)phosphinic acid / Esterase
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsCea Rama, I. / Sanz-Aparicio, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessProject BIO2016-76601-C3-3-R Spain
CitationJournal: Febs J. / Year: 2022
Title: Crystal structure of a family VIII beta-lactamase fold hydrolase reveals the molecular mechanism for its broad substrate scope.
Authors: Cea-Rama, I. / Coscolin, C. / Gonzalez-Alfonso, J.L. / Raj, J. / Vasiljevic, M. / Plou, F.J. / Ferrer, M. / Sanz-Aparicio, J.
History
DepositionSep 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase
B: Esterase
C: Esterase
D: Esterase
E: Esterase
F: Esterase
G: Esterase
H: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,25717
Polymers382,9388
Non-polymers2,3199
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA Analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19540 Å2
ΔGint-20 kcal/mol
Surface area103880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.541, 149.541, 321.718
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 8 - 409 / Label seq-ID: 27 - 428

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Esterase


Mass: 47867.230 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Plasmid: pBXNH3 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A2K8JQ66
#2: Chemical
ChemComp-P8K / hexyl(octoxy)phosphinic acid


Mass: 278.368 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C14H31O3P / Source: (gene. exp.) metagenome (others) / Plasmid: pBXNH3 / Production host: Escherichia coli MC1061 (bacteria) / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 24% PEG3350, 0.1M Bis-Tris propane 8.5, 0.2M NaF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2018 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.92→48.82 Å / Num. obs: 79916 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.046 / Net I/σ(I): 13.1
Reflection shellResolution: 2.92→2.98 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4498 / CC1/2: 0.896 / Rpim(I) all: 0.281 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PP3

7pp3


Resolution: 2.92→48.82 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 16.568 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4063 5.1 %RANDOM
Rwork0.1835 ---
obs0.1854 75753 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.58 Å2 / Biso mean: 60.092 Å2 / Biso min: 28.21 Å2
Baniso -1Baniso -2Baniso -3
1-3.11 Å20 Å20 Å2
2--3.11 Å20 Å2
3----6.21 Å2
Refinement stepCycle: final / Resolution: 2.92→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25208 0 6 83 25297
Biso mean--71.15 42.02 -
Num. residues----3216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01325797
X-RAY DIFFRACTIONr_bond_other_d0.0010.01723782
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.6534933
X-RAY DIFFRACTIONr_angle_other_deg1.2311.5955078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08653208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60221.4621368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.534154192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.88115192
X-RAY DIFFRACTIONr_chiral_restr0.0590.23248
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0229032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025648
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A136350.02
12B136350.02
21A136500.02
22C136500.02
31A136350.02
32D136350.02
41A136380.02
42E136380.02
51A136360.02
52F136360.02
61A136560.01
62G136560.01
71A136490.02
72H136490.02
81B136380.01
82C136380.01
91B136240.02
92D136240.02
101B136280.02
102E136280.02
111B136380.02
112F136380.02
121B136520.01
122G136520.01
131B136290.01
132H136290.01
141C136430.01
142D136430.01
151C136360.02
152E136360.02
161C136460.02
162F136460.02
171C136670.01
172G136670.01
181C136440.01
182H136440.01
191D136250.02
192E136250.02
201D136280.02
202F136280.02
211D136430.01
212G136430.01
221D136420.02
222H136420.02
231E136280.03
232F136280.03
241E136400.02
242G136400.02
251E136430.02
252H136430.02
261F136520.02
262G136520.02
271F136360.02
272H136360.02
281G136550.01
282H136550.01
LS refinement shellResolution: 2.92→2.996 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 297 -
Rwork0.3 5517 -
all-5814 -
obs--100 %

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