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- PDB-4qgp: Crystal structure of a pyrophosphatase (AF1178) from Archaeoglobu... -

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Basic information

Entry
Database: PDB / ID: 4qgp
TitleCrystal structure of a pyrophosphatase (AF1178) from Archaeoglobus fulgidus DSM 4304 at 1.80 A resolution
Componentspyrophosphatase
KeywordsHYDROLASE / dimeric four alpha-helical bundle / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / metal ion binding
Similarity search - Function
dCTP pyrophosphatase 1 / MazG-like family / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Uncharacterized protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.78 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a pyrophosphatase (AF1178) from Archaeoglobus fulgidus DSM 4304 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionJul 2, 2014ID: 3OBC
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pyrophosphatase
B: pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2269
Polymers28,7522
Non-polymers4747
Water1,856103
1
A: pyrophosphatase
B: pyrophosphatase
hetero molecules

A: pyrophosphatase
B: pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,45318
Polymers57,5044
Non-polymers94914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y,-z+1/21
Buried area18830 Å2
ΔGint-208 kcal/mol
Surface area19370 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-94 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.168, 102.136, 103.285
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-336-

HOH

21A-338-

HOH

31B-349-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein pyrophosphatase /


Mass: 14375.931 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_1178 / Plasmid: MH4a / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: O29089

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Non-polymers , 6 types, 110 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT (RESIDUES 1-106) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH.

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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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 63.0% polyethylene glycol 200, 0.2M magnesium chloride, 0.1M sodium cacodylate pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97954
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 2009 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979541
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.706
11-H, L, K20.294
ReflectionResolution: 1.8→28.202 Å / Num. obs: 24327 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.035 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.16
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.6051.578374184195.8
1.86-1.940.433294464952199
1.94-2.030.3012.989904718199.1
2.03-2.130.214.282744330198.9
2.13-2.270.1376.291474784198.4
2.27-2.440.1027.985584460198.6
2.44-2.690.0819.889564661198.1
2.69-3.070.05713.686424491197.7
3.07-3.870.0322.786094484196
3.87-28.20.02131.487024483195.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 30, 2009data scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.78→28.202 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.006 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. MAGNESIUM (MG), CHLORIDE (CL), AND POLYETHYLENE GLYCOL 200 FRAGMENTS (PG4 AND PGE) FROM THE CRYSTALLIZATION/CRYO CONDITIONS ARE MODELED INTO THE STRUCTURE. 4. THE DIFFRACTION DATA ARE PSEUDO-MEROHEDRALLY TWINNED WITH TWIN LAW (-H, L, K). THE REFINED TWIN FRACTION WAS 0.30. 6. REFLECTIONS FOR THE FREE-R SET WERE SELECTED BY RANDOM EXPANDED BY THE TWIN LAW. 7. NCS RESTRAINTS WERE APPLIED USING REFMAC'S LOCAL NCS OPT
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1230 5.1 %RANDOM
Rwork0.1935 ---
obs0.1956 24325 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 108.38 Å2 / Biso mean: 25.5229 Å2 / Biso min: 12.02 Å2
Baniso -1Baniso -2Baniso -3
1--20.86 Å2-0 Å2-0 Å2
2--4.07 Å20 Å2
3---16.79 Å2
Refinement stepCycle: LAST / Resolution: 1.78→28.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 28 103 1916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191923
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9712609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8235241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.02723.9100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05815351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0811515
X-RAY DIFFRACTIONr_chiral_restr0.10.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021443
X-RAY DIFFRACTIONr_mcbond_it1.8752.787886
X-RAY DIFFRACTIONr_mcangle_it2.485.2021111
X-RAY DIFFRACTIONr_scbond_it3.0743.4221034
LS refinement shellResolution: 1.781→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 50 -
Rwork0.196 1089 -
all-1139 -
obs--61.34 %
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)
10.60010.05770.0050.5253-0.14990.5806-0.01620.06070.0739-0.1050.0431-0.0097-0.06720.0247-0.02690.1416-0.00810.00640.10220.01540.0135.38297.975413.3497
20.96510.1402-0.11130.4843-0.21770.44170.01160.05410.0002-0.05190.01010.0199-0.0402-0.0235-0.02170.12860.004-0.00540.08670.01510.00416.749910.801116.5581
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 100
2X-RAY DIFFRACTION2B-6 - 100

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