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- PDB-7pp8: STRUCTURE OF ESTER-HYDROLASE EH7 FROM METAGENOME OF MARINE SEDIME... -

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Basic information

Entry
Database: PDB / ID: 7pp8
TitleSTRUCTURE OF ESTER-HYDROLASE EH7 FROM METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY) COMPLEXED WITH A DERIVATIVE OF METHYL 4-NITROPHENYL HEXYLPHOSPHONATE
ComponentsEsterase
KeywordsHYDROLASE / Ester Hydrolase / complex
Function / homology: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / methyl hydrogen (R)-hexylphosphonate / DI(HYDROXYETHYL)ETHER / Esterase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 13, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)385,03823
Polymers382,9388
Non-polymers2,10015
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA Analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20730 Å2
ΔGint-20 kcal/mol
Surface area106250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.641, 150.641, 325.261
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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNVALVALAA9 - 40828 - 427
21ASNASNVALVALBB9 - 40828 - 427
12SERSERASPASPAA8 - 40927 - 428
22SERSERASPASPCC8 - 40927 - 428
13ASNASNVALVALAA9 - 40828 - 427
23ASNASNVALVALDD9 - 40828 - 427
14SERSERASPASPAA8 - 40927 - 428
24SERSERASPASPEE8 - 40927 - 428
15ASNASNVALVALAA9 - 40828 - 427
25ASNASNVALVALFF9 - 40828 - 427
16SERSERASPASPAA8 - 40927 - 428
26SERSERASPASPGG8 - 40927 - 428
17ASNASNVALVALAA9 - 40828 - 427
27ASNASNVALVALHH9 - 40828 - 427
18ASNASNVALVALBB9 - 40828 - 427
28ASNASNVALVALCC9 - 40828 - 427
19ASNASNASPASPBB9 - 40928 - 428
29ASNASNASPASPDD9 - 40928 - 428
110ASNASNVALVALBB9 - 40828 - 427
210ASNASNVALVALEE9 - 40828 - 427
111ASNASNASPASPBB9 - 40928 - 428
211ASNASNASPASPFF9 - 40928 - 428
112ASNASNVALVALBB9 - 40828 - 427
212ASNASNVALVALGG9 - 40828 - 427
113ASNASNASPASPBB9 - 40928 - 428
213ASNASNASPASPHH9 - 40928 - 428
114ASNASNVALVALCC9 - 40828 - 427
214ASNASNVALVALDD9 - 40828 - 427
115SERSERASPASPCC8 - 40927 - 428
215SERSERASPASPEE8 - 40927 - 428
116ASNASNVALVALCC9 - 40828 - 427
216ASNASNVALVALFF9 - 40828 - 427
117SERSERASPASPCC8 - 40927 - 428
217SERSERASPASPGG8 - 40927 - 428
118ASNASNVALVALCC9 - 40828 - 427
218ASNASNVALVALHH9 - 40828 - 427
119ASNASNVALVALDD9 - 40828 - 427
219ASNASNVALVALEE9 - 40828 - 427
120ASNASNASPASPDD9 - 40928 - 428
220ASNASNASPASPFF9 - 40928 - 428
121ASNASNVALVALDD9 - 40828 - 427
221ASNASNVALVALGG9 - 40828 - 427
122ASNASNASPASPDD9 - 40928 - 428
222ASNASNASPASPHH9 - 40928 - 428
123ASNASNVALVALEE9 - 40828 - 427
223ASNASNVALVALFF9 - 40828 - 427
124SERSERASPASPEE8 - 40927 - 428
224SERSERASPASPGG8 - 40927 - 428
125ASNASNVALVALEE9 - 40828 - 427
225ASNASNVALVALHH9 - 40828 - 427
126ASNASNVALVALFF9 - 40828 - 427
226ASNASNVALVALGG9 - 40828 - 427
127ASNASNASPASPFF9 - 40928 - 428
227ASNASNASPASPHH9 - 40928 - 428
128ASNASNVALVALGG9 - 40828 - 427
228ASNASNVALVALHH9 - 40828 - 427

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.) uncultured bacterium (environmental samples)
Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A2K8JQ66
#2: Chemical
ChemComp-MHH / methyl hydrogen (R)-hexylphosphonate


Mass: 180.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H17O3P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49.04 %
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: 2.65→49.68 Å / Num. obs: 107165 / % possible obs: 98.4 % / Redundancy: 5.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.043 / Net I/σ(I): 13
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5270 / CC1/2: 0.76 / Rpim(I) all: 0.326 / % possible all: 98.6

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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: 2.65→49.68 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.052 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 5.4 / ESU R Free: 0.293
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 5373 5 %RANDOM
Rwork0.196 ---
obs0.1971 101698 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.28 Å2 / Biso mean: 44.907 Å2 / Biso min: 21.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2--1.52 Å20 Å2
3----3.03 Å2
Refinement stepCycle: final / Resolution: 2.65→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25128 0 43 192 25363
Biso mean--68.72 35.73 -
Num. residues----3212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01325748
X-RAY DIFFRACTIONr_bond_other_d0.0020.01723693
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.6534875
X-RAY DIFFRACTIONr_angle_other_deg1.2471.58254849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67453204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84221.4621368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.772154188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.07915192
X-RAY DIFFRACTIONr_chiral_restr0.0650.23244
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0229004
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025644
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A131560.04
12B131560.04
21A131790.05
22C131790.05
31A131760.04
32D131760.04
41A132700.02
42E132700.02
51A131530.03
52F131530.03
61A131430.05
62G131430.05
71A131580.04
72H131580.04
81B131800.04
82C131800.04
91B132050.04
92D132050.04
101B131290.04
102E131290.04
111B132800.03
112F132800.03
121B131830.04
122G131830.04
131B132040.03
132H132040.03
141C131460.04
142D131460.04
151C131430.05
152E131430.05
161C131780.04
162F131780.04
171C132450.03
172G132450.03
181C131540.04
182H131540.04
191D131280.03
192E131280.03
201D131850.04
202F131850.04
211D131180.04
212G131180.04
221D132430.02
222H132430.02
231E131300.03
232F131300.03
241E131550.05
242G131550.05
251E131450.03
252H131450.03
261F131670.04
262G131670.04
271F131950.03
272H131950.03
281G131420.04
282H131420.04
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 392 -
Rwork0.313 7456 -
all-7848 -
obs--98.52 %

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