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- PDB-2pq7: Crystal structure of predicted HD superfamily hydrolase (10416199... -

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Basic information

Entry
Database: PDB / ID: 2pq7
TitleCrystal structure of predicted HD superfamily hydrolase (104161995) from uncultured Thermotogales bacterium at 1.45 A resolution
ComponentsPredicted HD superfamily hydrolase
KeywordsHYDROLASE / 104161995 / HD domain / predicted HD superfamily hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
HDIG domain / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PHOSPHATE ION / Predicted HD superfamily hydrolase
Similarity search - Component
Biological speciesuncultured Thermotogales bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of predicted HD superfamily hydrolase (104161995) from uncultured Thermotogales bacterium at 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted HD superfamily hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4187
Polymers24,9621
Non-polymers4556
Water2,666148
1
A: Predicted HD superfamily hydrolase
hetero molecules

A: Predicted HD superfamily hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,83514
Polymers49,9252
Non-polymers91112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)138.518, 40.662, 37.789
Angle α, β, γ (deg.)90.000, 95.320, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Predicted HD superfamily hydrolase


Mass: 24962.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured Thermotogales bacterium (environmental samples)
Gene: 104161995, mes0020 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1EM40

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Non-polymers , 5 types, 154 molecules

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


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: NANODROP, 24.0% 2-methyl-2,4-pentanediol, 0.2M Sodium chloride, 0.1M Sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97916, 0.97867
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 14, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979161
30.978671
ReflectionResolution: 1.45→27.441 Å / Num. obs: 37299 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.32 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.45-1.493.70.7011.1983726950.70199.8
1.49-1.533.70.5751.3974526610.57599.8
1.53-1.573.70.4391.7967226370.43999.7
1.57-1.623.70.3512.2925825250.351100
1.62-1.673.70.2952.5896324340.29599.9
1.67-1.733.70.2423.1878223810.242100
1.73-1.83.70.1963.8852722970.196100
1.8-1.873.70.1644.6816921970.164100
1.87-1.963.70.1295.8790621290.129100
1.96-2.053.70.1076.8752820270.107100
2.05-2.163.70.0769.3713919090.076100
2.16-2.293.70.0699.9679018230.069100
2.29-2.453.70.06510.2641717210.065100
2.45-2.653.70.05511.8603416220.055100
2.65-2.93.70.04913.3557514930.049100
2.9-3.243.70.04613.3492313210.046100
3.24-3.743.70.04612.7446912050.046100
3.74-4.593.70.03717.7368510050.037100
4.59-6.483.60.03816.528337930.03899.9
6.48-27.443.20.04513.413564240.04593.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→27.441 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.373 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.061
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TWO IRON IONS, ONE CHLORIDE ION, TWO PHOSPHATE IONS AND ONE 2-METHYL-2,4-PENTANEDIOL WERE MODELED. THE PRESENCE OF THE TWO IRON ATOMS IS SUPPORTED BY X-RAY FLUORESCENCE MEASUREMENTS, ANOMALOUS DIFFERENCE FOURIERS AND GEOMETRY. 5. RESIDUES 113 TO 117, 148 TO 185 ARE DISORDERED AND NOT MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1864 5 %RANDOM
Rwork0.183 ---
all0.183 ---
obs0.183 37299 99.85 %-
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 mean: 20.351 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.96 Å2
2---1.13 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.45→27.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 13 156 1613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221496
X-RAY DIFFRACTIONr_bond_other_d0.0020.021381
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9532038
X-RAY DIFFRACTIONr_angle_other_deg0.98633191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5365197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.74223.16760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71415254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2651510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021692
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02312
X-RAY DIFFRACTIONr_nbd_refined0.2180.3411
X-RAY DIFFRACTIONr_nbd_other0.1560.31404
X-RAY DIFFRACTIONr_nbtor_refined0.1830.5789
X-RAY DIFFRACTIONr_nbtor_other0.0890.5858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.5197
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.349
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.529
X-RAY DIFFRACTIONr_mcbond_it2.2183983
X-RAY DIFFRACTIONr_mcbond_other0.5243382
X-RAY DIFFRACTIONr_mcangle_it3.00351536
X-RAY DIFFRACTIONr_scbond_it5.6418584
X-RAY DIFFRACTIONr_scangle_it7.85911501
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 142 -
Rwork0.297 2554 -
obs-2696 99.81 %

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