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- PDB-3mdq: Crystal structure of an Exopolyphosphatase (CHU_0316) from Cytoph... -

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Basic information

Entry
Database: PDB / ID: 3mdq
TitleCrystal structure of an Exopolyphosphatase (CHU_0316) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution
ComponentsExopolyphosphatase
KeywordsHYDROLASE / Exopolyphosphatase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


exopolyphosphatase / exopolyphosphatase activity
Similarity search - Function
: / Ppx/GppA phosphatase / Ppx/GppA phosphatase family / Exopolyphosphatase. Domain 2 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Exopolyphosphatase / Exopolyphosphatase
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an Exopolyphosphatase (CHU_0316) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,50910
Polymers35,7771
Non-polymers7319
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.687, 89.335, 89.374
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Exopolyphosphatase


Mass: 35777.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / NCIMB 9469 / Gene: ppx, CHU_0316 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q11YA9, UniProt: A0A6N4SMU8*PLUS, exopolyphosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.4500M ammonium sulfate, 13.6000% Glycerol, 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: 0.96109,0.97934,0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 11, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961091
20.979341
30.979251
ReflectionResolution: 1.5→29.786 Å / Num. obs: 56714 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.011 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.14
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.550.4351.7176529366190.3
1.55-1.620.3452.22322212150197.5
1.62-1.690.2582.91982610243196.9
1.69-1.780.2073.62108210801196.3
1.78-1.890.14652074310494195.7
1.89-2.040.0947.52163810822195
2.04-2.240.06910.42028010067193.9
2.24-2.560.05612.52082510277193.1
2.56-3.230.04216.22124810344192.1
3.23-29.7860.03520.6207799976189.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.786 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 2.473 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (3) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (3) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF 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. (4) CHLORIDE (CL) AND SULFATE (SO4) IONS FROM CRYSTALLIZATION CONDITION, AND GLYCEROL (GOL) MOLECULES FROM EITHER CRYSTALLIZATION OR CRYO CONDITION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2875 5.1 %RANDOM
Rwork0.153 ---
obs0.154 56672 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.47 Å2 / Biso mean: 17.122 Å2 / Biso min: 5.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.29 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 40 350 2798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222740
X-RAY DIFFRACTIONr_bond_other_d0.0010.021796
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9643737
X-RAY DIFFRACTIONr_angle_other_deg0.95734420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4555362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53724.37119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4415494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.651519
X-RAY DIFFRACTIONr_chiral_restr0.0960.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023123
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02534
X-RAY DIFFRACTIONr_mcbond_it1.66431715
X-RAY DIFFRACTIONr_mcbond_other0.4363699
X-RAY DIFFRACTIONr_mcangle_it2.81252807
X-RAY DIFFRACTIONr_scbond_it4.54681025
X-RAY DIFFRACTIONr_scangle_it7.05711930
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 219 -
Rwork0.253 3862 -
all-4081 -
obs--95.11 %
Refinement TLS params.Method: refined / Origin x: 35.3504 Å / Origin y: 4.7463 Å / Origin z: 69.2282 Å
111213212223313233
T0.0021 Å20.0012 Å20.0009 Å2-0.0027 Å2-0.0006 Å2--0.0061 Å2
L0.2309 °20.098 °20.035 °2-0.3265 °20.108 °2--0.4532 °2
S0.0023 Å °-0.0091 Å °0.0112 Å °-0.0038 Å °0.0018 Å °0.0093 Å °-0.0198 Å °0.0033 Å °-0.0042 Å °

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