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- PDB-8wzu: 4-hydroxybutyryl-CoA Synthetase (ADP-forming) from Nitrosopumilus... -

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Basic information

Entry
Database: PDB / ID: 8wzu
Title4-hydroxybutyryl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus.
Components4-hydroxybutyrate--CoA ligase [ADP-forming]
KeywordsLIGASE / Nitropumilus maritimus / ACD / Synthetase / HB/HP / carbon fixation / thaumarchaeota
Function / homology
Function and homology information


4-hydroxybutyrate-CoA ligase (ADP-forming) / acetate-CoA ligase (ADP-forming) activity / ATP binding / metal ion binding
Similarity search - Function
Ligase-CoA domain / ATP-grasp domain / Ligase-CoA domain / Succinyl-CoA synthetase-like, flavodoxin domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ATP-grasp fold, subdomain 1 ...Ligase-CoA domain / ATP-grasp domain / Ligase-CoA domain / Succinyl-CoA synthetase-like, flavodoxin domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ATP-grasp fold, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile. / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
4-hydroxybutyrate--CoA ligase [ADP-forming]
Similarity search - Component
Biological speciesNitrosopumilus maritimus SCM1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJohnson, J. / Demirci, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: To Be Published
Title: Crystal Structure of 4-hydroxybutyryl CoA synthetase (ADP-forming): A Key Enzyme in the Thaumarchaeal Hydroxypropionate/Hydroxybutyrate cycle.
Authors: Johnson, J. / Demirci, H.
History
DepositionNov 2, 2023Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 12, 2024ID: 8IUP
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxybutyrate--CoA ligase [ADP-forming]
B: 4-hydroxybutyrate--CoA ligase [ADP-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,6484
Polymers151,4562
Non-polymers1922
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-73 kcal/mol
Surface area50900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)356.980, 70.400, 75.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein 4-hydroxybutyrate--CoA ligase [ADP-forming] / 4-hydroxybutyryl-coenzyme A synthetase [ADP-forming] / 4-hydroxybutyryl-CoA synthetase [ADP-forming]


Mass: 75727.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosopumilus maritimus SCM1 (archaea)
Gene: Nmar_0206 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: A9A1Y1, 4-hydroxybutyrate-CoA ligase (ADP-forming)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: 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: 3.14 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: pH 4.5, 100mM Na-acetate/acetic acid, 200mM lithium sulfate, 50% (v/v) PEG 400, 0.5uL of 100% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.73 - 1.85
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.731
21.851
ReflectionResolution: 2.69→24.88 Å / Num. obs: 53788 / % possible obs: 98 % / Redundancy: 13.16 % / Biso Wilson estimate: 51.3 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.49
Reflection shellResolution: 2.69→2.75 Å / Redundancy: 11.77 % / Mean I/σ(I) obs: 0.59 / Num. unique obs: 7963 / CC1/2: 0.27 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMACv5.5refinement
XDSdata reduction
Aimless0.5.31data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→24.88 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.881 / SU B: 39.626 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R: 1.281 / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 2992 6.8 %RANDOM
Rwork0.23618 ---
obs0.23921 41150 91.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.844 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å2-0 Å2
2---3.2 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9479 0 10 83 9572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0179622
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169816
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.85512954
X-RAY DIFFRACTIONr_angle_other_deg0.4581.5722769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6725.1331281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.281101907
X-RAY DIFFRACTIONr_chiral_restr0.120.21536
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021817
X-RAY DIFFRACTIONr_mcbond_it2.7413.7094997
X-RAY DIFFRACTIONr_mcbond_other2.7413.7094997
X-RAY DIFFRACTIONr_mcangle_it4.6156.6726241
X-RAY DIFFRACTIONr_mcangle_other4.6156.6726242
X-RAY DIFFRACTIONr_scbond_it2.5813.9444625
X-RAY DIFFRACTIONr_scbond_other2.5763.9394617
X-RAY DIFFRACTIONr_scangle_other4.3877.1626702
X-RAY DIFFRACTIONr_long_range_B_refined8.96343.7840351
X-RAY DIFFRACTIONr_long_range_B_other8.95743.7940335
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 184 -
Rwork0.372 2379 -
obs--74.7 %
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)
11.2859-0.16930.08451.44230.09790.8095-0.02540.0906-0.094-0.05960.01730.17080.13310.03950.00820.03220.03520.00060.25330.03670.031156.40623.314.428
21.7501-0.4543-0.20441.53660.15880.8774-0.1207-0.18860.27050.19040.04030.0484-0.13890.09790.08040.0801-0.0708-0.05490.26280.06090.108753.76459.0624.982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 698
2X-RAY DIFFRACTION2B1 - 698

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