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- PDB-5c9g: Crystal Structure of a Putative enoyl-CoA hydratase/isomerase fam... -

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Basic information

Entry
Database: PDB / ID: 5c9g
TitleCrystal Structure of a Putative enoyl-CoA hydratase/isomerase family protein from Hyphomonas neptunium
ComponentsEnoyl-CoA hydratase/isomerase family protein
KeywordsISOMERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


fatty acid beta-oxidation / isomerase activity / lyase activity
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
D-MALATE / Enoyl-CoA hydratase/isomerase family protein
Similarity search - Component
Biological speciesHyphomonas neptunium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSzlachta, K. / Cooper, D.R. / Chapman, H.C. / Cymbrowski, M.T. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Bonanno, J. / Seidel, R. / Almo, S.C. ...Szlachta, K. / Cooper, D.R. / Chapman, H.C. / Cymbrowski, M.T. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / Hammonds, J. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal Structure of a Putative enoyl-CoA hydratase/isomerase family protein from Hyphomonas neptunium
Authors: Szlachta, K. / Cooper, D.R. / Chapman, H.C. / Cymbrowski, M.T. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / Hammonds, J. / New York ...Authors: Szlachta, K. / Cooper, D.R. / Chapman, H.C. / Cymbrowski, M.T. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / Hammonds, J. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionJun 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_oper_list
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: 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 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein
C: Enoyl-CoA hydratase/isomerase family protein
D: Enoyl-CoA hydratase/isomerase family protein
E: Enoyl-CoA hydratase/isomerase family protein
F: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,7308
Polymers181,4016
Non-polymers3282
Water20,7711153
1
A: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein
C: Enoyl-CoA hydratase/isomerase family protein


Theoretical massNumber of molelcules
Total (without water)90,7013
Polymers90,7013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-83 kcal/mol
Surface area31050 Å2
MethodPISA
2
D: Enoyl-CoA hydratase/isomerase family protein
E: Enoyl-CoA hydratase/isomerase family protein
F: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0295
Polymers90,7013
Non-polymers3282
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-86 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.479, 128.120, 209.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

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
11SERSERTYRTYRAA0 - 25922 - 281
21SERSERTYRTYRBB0 - 25922 - 281
12THRTHRTYRTYRAA2 - 25924 - 281
22THRTHRTYRTYRCC2 - 25924 - 281
13GLYGLYARGARGAA-12 - 26010 - 282
23GLYGLYARGARGDD-12 - 26010 - 282
14THRTHRTYRTYRAA2 - 25924 - 281
24THRTHRTYRTYREE2 - 25924 - 281
15GLNGLNTYRTYRAA-1 - 25921 - 281
25GLNGLNTYRTYRFF-1 - 25921 - 281
16THRTHRTYRTYRBB2 - 25924 - 281
26THRTHRTYRTYRCC2 - 25924 - 281
17SERSERTYRTYRBB0 - 25922 - 281
27SERSERTYRTYRDD0 - 25922 - 281
18THRTHRTYRTYRBB2 - 25924 - 281
28THRTHRTYRTYREE2 - 25924 - 281
19SERSERTYRTYRBB0 - 25922 - 281
29SERSERTYRTYRFF0 - 25922 - 281
110THRTHRTYRTYRCC2 - 25924 - 281
210THRTHRTYRTYRDD2 - 25924 - 281
111THRTHRARGARGCC2 - 26024 - 282
211THRTHRARGARGEE2 - 26024 - 282
112THRTHRTYRTYRCC2 - 25924 - 281
212THRTHRTYRTYRFF2 - 25924 - 281
113THRTHRTYRTYRDD2 - 25924 - 281
213THRTHRTYRTYREE2 - 25924 - 281
114GLNGLNTYRTYRDD-1 - 25921 - 281
214GLNGLNTYRTYRFF-1 - 25921 - 281
115THRTHRTYRTYREE2 - 25924 - 281
215THRTHRTYRTYRFF2 - 25924 - 281

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Enoyl-CoA hydratase/isomerase family protein


Mass: 30233.537 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyphomonas neptunium (strain ATCC 15444) (bacteria)
Strain: ATCC 15444 / Gene: HNE_1107 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q0C365
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1153 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 ul of 17.6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of (the JCSG+ condition #G8) 0.15M DL-Malic acid, 19% ...Details: 0.2 ul of 17.6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of (the JCSG+ condition #G8) 0.15M DL-Malic acid, 19% PEG 3350 and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 98973 / % possible obs: 97.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.055 / Rrim(I) all: 0.14 / Χ2: 1.159 / Net I/av σ(I): 14.857 / Net I/σ(I): 4.8 / Num. measured all: 726544
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.1-2.146.947790.7470.4720.66495.2
2.14-2.187.147630.790.4340.6595.6
2.18-2.227.147750.8410.3770.67295.90.981
2.22-2.267.248090.8840.2430.68995.90.6350.682
2.26-2.317.248220.90.2720.69696.70.710.762
2.31-2.377.248400.9250.2250.71796.20.5870.63
2.37-2.427.248510.9460.1990.72397.30.5180.556
2.42-2.497.248710.9520.1730.73497.30.4510.484
2.49-2.567.249010.9610.1530.77996.90.3990.428
2.56-2.657.248730.9720.1250.897.20.3260.35
2.65-2.747.249170.980.1060.84297.80.2760.297
2.74-2.857.349120.9850.0860.90397.50.2250.241
2.85-2.987.349370.990.0730.94597.90.1890.203
2.98-3.147.349680.9920.061.05198.20.1560.167
3.14-3.337.450310.9950.0471.2498.80.1240.133
3.33-3.597.550490.9960.0391.52599.70.1030.11
3.59-3.957.751150.9950.0372.0671000.0960.103
3.95-4.527.951400.9970.0332.5731000.0870.093
4.52-5.7851900.9970.0292.1911000.0790.084
5.7-407.654300.9990.021.89199.90.0530.057

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-3000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data collection
MOLREPphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OLQ

4olq


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2091 / WRfactor Rwork: 0.177 / FOM work R set: 0.8058 / SU B: 10.332 / SU ML: 0.14 / SU R Cruickshank DPI: 0.2367 / SU Rfree: 0.1855 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.186
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 4923 5 %RANDOM
Rwork0.1984 ---
obs0.2 93373 97.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.38 Å2 / Biso mean: 33.663 Å2 / Biso min: 15.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0 Å20 Å2
2--1.29 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11687 0 22 1153 12862
Biso mean--66.59 37.01 -
Num. residues----1587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911916
X-RAY DIFFRACTIONr_bond_other_d0.0090.0211648
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.97416147
X-RAY DIFFRACTIONr_angle_other_deg1.576326678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65351583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60423.547468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.683151834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6831593
X-RAY DIFFRACTIONr_chiral_restr0.0750.21841
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113704
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022613
X-RAY DIFFRACTIONr_mcbond_it1.292.8456344
X-RAY DIFFRACTIONr_mcbond_other1.292.8456343
X-RAY DIFFRACTIONr_mcangle_it2.1284.2617920
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A289460.08
12B289460.08
21A286840.08
22C286840.08
31A311000.04
32D311000.04
41A288720.09
42E288720.09
51A287760.08
52F287760.08
61B295520.08
62C295520.08
71B297440.08
72D297440.08
81B296960.08
82E296960.08
91B302140.07
92F302140.07
101C295520.08
102D295520.08
111C304380.05
112E304380.05
121C294160.09
122F294160.09
131D296560.09
132E296560.09
141D296160.08
142F296160.08
151E293960.09
152F293960.09
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 348 -
Rwork0.291 6593 -
all-6941 -
obs--95.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.2877-0.17120.19930.129-0.12560.1437-0.0319-0.0466-0.06930.0150.0660.0261-0.0323-0.0446-0.03410.02550.00930.00860.06080.00050.0422-9.53721.359715.6612
20.2549-0.0470.16730.1339-0.0620.361-0.0398-0.01430.02930.01420.0009-0.0107-0.03880.02920.03890.03130.0095-0.00930.0347-0.01040.009821.377433.133824.3619
30.35810.26490.07650.3444-0.06190.2146-0.00620.0198-0.00460.02470.03190.01530.04560.0156-0.02560.04960.0233-0.00190.0244-0.00680.00712.12944.52937.5844
40.03460.0130.07370.07410.03140.16720.00140.0043-0.0084-0.01010.01940.00780.00350.0308-0.02080.0149-0.0071-0.00030.0505-0.00710.030329.936321.404988.4303
50.4976-0.20850.09590.313-0.02760.13560.02520.002-0.0276-0.0067-0.0007-0.00170.0567-0.02-0.02440.0367-0.018-0.010.02150.00240.00528.41164.876667.1701
60.33060.09150.15420.20540.09470.1991-0.04120.02060.052-0.02270.01680.016-0.0045-0.00720.02440.0274-0.0084-0.00320.03110.01150.0117-1.284733.536280.5854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-12 - 260
2X-RAY DIFFRACTION2B-10 - 260
3X-RAY DIFFRACTION3C2 - 260
4X-RAY DIFFRACTION4D-12 - 260
5X-RAY DIFFRACTION5E2 - 260
6X-RAY DIFFRACTION6F-3 - 260

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