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- PDB-3hc1: Crystal structure of HDOD domain protein with unknown function (N... -

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Basic information

Entry
Database: PDB / ID: 3hc1
TitleCrystal structure of HDOD domain protein with unknown function (NP_953345.1) from GEOBACTER SULFURREDUCENS at 1.90 A resolution
Componentsuncharacterized HDOD domain protein
Keywordsstructural genomics / unknown function / NP_953345.1 / HDOD domain protein with unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / Metal-dependent hydrolase HDOD / HDOD domain / HD-related output (HDOD) domain profile. / Hypothetical protein af1432 / Hypothetical protein af1432 / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / Metal-dependent phosphohydrolase, HDOD domain-containing
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of HDOD domain protein with unknown function (NP_953345.1) from GEOBACTER SULFURREDUCENS at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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 6, 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: uncharacterized HDOD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5279
Polymers33,9721
Non-polymers5558
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.567, 66.631, 54.412
Angle α, β, γ (deg.)90.000, 111.960, 90.000
Int Tables number4
Space group name H-MP1211
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE STATE IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein uncharacterized HDOD domain protein / HD domain protein


Mass: 33972.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: GSU2296, NP_953345.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q74AQ6

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Non-polymers , 5 types, 173 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2000M KThioCyanate, 20.0000% PEG-3350, No Buffer pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97932,0.97911
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2009 / 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
10.918371
20.979321
30.979111
ReflectionResolution: 1.9→28.375 Å / Num. obs: 24939 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 23.082 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.953.80.7611.9689418200.761100
1.95-23.80.5742.5686218040.574100
2-2.063.80.4223.5656317250.422100
2.06-2.123.80.3653.9638216780.365100
2.12-2.193.80.2855631816560.285100
2.19-2.273.80.2465.7605315880.246100
2.27-2.363.80.2186.3582115250.218100
2.36-2.453.80.1717.9558314630.171100
2.45-2.563.80.1459.1544314230.145100
2.56-2.693.80.11811.2518613550.118100
2.69-2.833.80.10212.8494412920.102100
2.83-33.80.09214.5467812230.092100
3-3.213.80.07818.1437911470.078100
3.21-3.473.80.06221.5406010620.062100
3.47-3.83.80.05125.737679860.051100
3.8-4.253.80.04330.234238990.043100
4.25-4.913.80.043130417980.04100
4.91-6.013.80.04329.525696790.043100
6.01-8.53.70.03930.819445190.039100
8.5-28.383.60.0373410632970.03797.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→28.375 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.555 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.143
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. GLYCEROL, POTASSIUM AND CHLORIDE MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 5. THE PRESENCE OF FE IONS WERE CONFIRMED BY ANOMALOUS DIFFERENCE FOURIERS AND X-RAY FLUORESCENCE EXPERIMENTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1268 5.1 %RANDOM
Rwork0.18 ---
obs0.182 24920 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.65 Å2 / Biso mean: 26.721 Å2 / Biso min: 2.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20.71 Å2
2--1.04 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 28 165 2505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222432
X-RAY DIFFRACTIONr_bond_other_d0.0030.021618
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9753317
X-RAY DIFFRACTIONr_angle_other_deg1.0633953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2175314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62923.551107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37515401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4431518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022715
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02504
X-RAY DIFFRACTIONr_mcbond_it2.05431512
X-RAY DIFFRACTIONr_mcbond_other0.5953613
X-RAY DIFFRACTIONr_mcangle_it3.17952451
X-RAY DIFFRACTIONr_scbond_it5.4418920
X-RAY DIFFRACTIONr_scangle_it7.65511858
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 92 -
Rwork0.269 1721 -
all-1813 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: -2.254 Å / Origin y: 31.3479 Å / Origin z: 21.8305 Å
111213212223313233
T0.0093 Å2-0.0011 Å20.0029 Å2-0.0081 Å2-0.0014 Å2--0.0032 Å2
L2.0054 °2-0.0966 °20.0314 °2-0.8397 °20.2026 °2--0.7802 °2
S0.0214 Å °0.1005 Å °0.0185 Å °-0.0287 Å °0.0084 Å °-0.0422 Å °0.0131 Å °0.0421 Å °-0.0298 Å °

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