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- PDB-1jhd: Crystal Structure of Bacterial ATP Sulfurylase from the Riftia pa... -

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Basic information

Entry
Database: PDB / ID: 1jhd
TitleCrystal Structure of Bacterial ATP Sulfurylase from the Riftia pachyptila Symbiont
ComponentsSULFATE ADENYLYLTRANSFERASE
KeywordsTRANSFERASE / adenylyl transferase / sulfurylase / aps / chemoautotroph / bromide
Function / homology
Function and homology information


sulfate adenylyltransferase / sulfate adenylyltransferase (ATP) activity / sulfate assimilation / hydrogen sulfide biosynthetic process / ATP binding
Similarity search - Function
Sulphate adenylyltransferase, prokaryotic-type / Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / PUA-like superfamily / HUPs ...Sulphate adenylyltransferase, prokaryotic-type / Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / PUA-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Sulfate adenylyltransferase
Similarity search - Component
Biological speciesSulfur-oxidizing endosymbiont of Riftia pachyptila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsBeynon, J.D. / MacRae, I.J. / Huston, S.L. / Nelson, D.C. / Segel, I.H. / Fisher, A.J.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structure of ATP sulfurylase from the bacterial symbiont of the hydrothermal vent tubeworm Riftia pachyptila.
Authors: Beynon, J.D. / MacRae, I.J. / Huston, S.L. / Nelson, D.C. / Segel, I.H. / Fisher, A.J.
History
DepositionJun 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: SULFATE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,86912
Polymers43,9421
Non-polymers92711
Water8,971498
1
A: SULFATE ADENYLYLTRANSFERASE
hetero molecules

A: SULFATE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,73924
Polymers87,8842
Non-polymers1,85522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)59.561, 75.546, 95.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein SULFATE ADENYLYLTRANSFERASE / E.C.2.7.7.4 / Chemoautotropic Bacterial ATP Sulfurylase / SULFATE ADENYLATE TRANSFERASE / SAT / ATP-SULFURYLASE


Mass: 43941.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfur-oxidizing endosymbiont of Riftia pachyptila (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q54506, sulfate adenylyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, 2.3M Ammonium Sulfate, 2% PEG 400, 100mM NaBr, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 300K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
22.3 Mammonium sulfate1reservoir
3100 mM1reservoirNaBr
42 %PEG4001reservoir
5100 mMsodium HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9197 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 2000
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 48942 / Num. obs: 46914 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.15 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 15.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.61 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 5.3 / % possible all: 71.7

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.78 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1591193.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2418 5.2 %RANDOM
Rwork0.167 ---
obs0.167 46759 96.6 %-
all-48942 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.64 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2---1 Å20 Å2
3----0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3078 0 23 498 3599
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.251.5
X-RAY DIFFRACTIONc_mcangle_it2.872
X-RAY DIFFRACTIONc_scbond_it3.692
X-RAY DIFFRACTIONc_scangle_it5.242.5
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.277 178 4.7 %
Rwork0.207 3613 -
obs--79.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.23
X-RAY DIFFRACTIONc_mcbond_it2.251.5
X-RAY DIFFRACTIONc_scbond_it3.692
X-RAY DIFFRACTIONc_mcangle_it2.872
X-RAY DIFFRACTIONc_scangle_it5.242.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.277 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.207

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