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- PDB-2w4d: Acylphosphatase variant G91A from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 2w4d
TitleAcylphosphatase variant G91A from Pyrococcus horikoshii
ComponentsACYLPHOSPHATASE
KeywordsHYDROLASE
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity / hydrolase activity
Similarity search - Function
Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits ...Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Acylphosphatase
Similarity search - Component
Biological speciesPYROCOCCUS HORIKOSHII (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLam, S.Y. / Wong, K.B.
Citation
Journal: Plos Biol. / Year: 2011
Title: A Rigidifying Salt-Bridge Favors the Activity of Thermophilic Enzyme at High Temperatures at the Expense of Low-Temperature Activity.
Authors: Lam, S.Y. / Yeung, R.C.Y. / Yu, T. / Sze, K. / Wong, K.B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and Preliminary Crystallographic Analysis of an Acylphosphatase from the Hyperthermophilic Archaeon Pyrococcus Horikoshii
Authors: Cheung, Y.Y. / Allen, M.D. / Bycroft, M. / Wong, K.B.
#2: Journal: Biochemistry / Year: 2005
Title: Crystal Structure of a Hyperthermophilic Archaeal Acylphosphatase from Pyrococcus Horikoshii--Structural Insights Into Enzymatic Catalysis, Thermostability, and Dimerization.
Authors: Cheung, Y. / Lam, S.Y. / Chu, W. / Allen, M.D. / Bycroft, M. / Wong, K.
History
DepositionNov 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACYLPHOSPHATASE
B: ACYLPHOSPHATASE
C: ACYLPHOSPHATASE
D: ACYLPHOSPHATASE
E: ACYLPHOSPHATASE
F: ACYLPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,85719
Polymers60,9586
Non-polymers89913
Water2,252125
1
A: ACYLPHOSPHATASE
B: ACYLPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7228
Polymers20,3192
Non-polymers4026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-9.1 kcal/mol
Surface area10560 Å2
MethodPQS
2
C: ACYLPHOSPHATASE
D: ACYLPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5886
Polymers20,3192
Non-polymers2684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-10 kcal/mol
Surface area10740 Å2
MethodPQS
3
E: ACYLPHOSPHATASE
F: ACYLPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5485
Polymers20,3192
Non-polymers2293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-8.4 kcal/mol
Surface area10630 Å2
MethodPQS
Unit cell
Length a, b, c (Å)87.375, 153.526, 46.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
ACYLPHOSPHATASE / ACYLPHOSPHATE PHOSPHOHYDROLASE


Mass: 10159.682 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-91 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / Strain: JCM9974 / Plasmid: PET3A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P84142, acylphosphatase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 91 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLY 91 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLY 91 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLY 91 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLY 91 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLY 91 TO ALA ENGINEERED RESIDUE IN CHAIN E, GLY 91 TO ALA ENGINEERED RESIDUE IN CHAIN F, GLY 91 TO ALA

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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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 8.5
Details: 7.9MG/ML PROTEIN, 0.6M NA/K GRID SCREEN, PH8.5, CRYOPROTECTANT: 25% GLYCEROL

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 20, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.4→44.18 Å / Num. obs: 24753 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 2.92 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.74 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.2 / % possible all: 97.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W2I

1w2i


Resolution: 2.4→23.44 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1417720.6 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1253 5.1 %RANDOM
Rwork0.227 ---
obs0.227 24696 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.35 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-9.27 Å20 Å20 Å2
2---7.08 Å20 Å2
3----2.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→23.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4308 0 41 125 4474
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 192 4.8 %
Rwork0.259 3789 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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