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- PDB-3bdi: Crystal structure of predicted CIB-like hydrolase (NP_393672.1) f... -

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Basic information

Entry
Database: PDB / ID: 3bdi
TitleCrystal structure of predicted CIB-like hydrolase (NP_393672.1) from Thermoplasma acidophilum at 1.45 A resolution
ComponentsUncharacterized protein Ta0194
KeywordsHYDROLASE / NP_393672.1 / predicted CIB-like hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of predicted CIB-like hydrolase (NP_393672.1) from Thermoplasma acidophilum at 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: 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 1.4Jan 25, 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
Remark 999 SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 1. 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. 2. DNA SEQUENCING OF THE CLONED CONSTRUCT REVEALS A GLU AT POSITION 190 INSTEAD OF LYS. THIS IS CONSISTENT WITH THE OBSERVED ELECTRON DENSITY AT THIS POSITION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Ta0194
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8354
Polymers23,5171
Non-polymers3183
Water3,657203
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.384, 46.292, 101.644
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 Uncharacterized protein Ta0194


Mass: 23516.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Species: Thermoplasma acidophilum / Strain: DSM 1728, AMRC-C165, IFO 15155, JCM 9062 / Gene: NP_393672.1, Ta0194 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9HLN3
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. REMARK 999 DNA SEQUENCING OF THE CLONED CONSTRUCT REVEALS A GLU AT POSITION REMARK 999 190 INSTEAD OF LYS. THIS IS CONSISTENT WITH THE OBSERVED ELECTRON REMARK 999 DENSITY AT THIS POSITION. REMARK 999

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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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 5.0% PEG 3000, 44.0% PEG 400, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.94939, 0.97939, 0.97953
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.949391
20.979391
30.979531
ReflectionResolution: 1.45→27.338 Å / Num. obs: 37089 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 3.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.45-1.492.50.1943.5665926760.19499.9
1.49-1.533.20.193.7836726140.19100
1.53-1.573.60.174.1928025800.17100
1.57-1.623.60.1434.7900724990.143100
1.62-1.673.60.135.2877624300.13100
1.67-1.733.60.1215.5841623270.121100
1.73-1.83.60.1125.7819422560.112100
1.8-1.873.60.1066.1794121960.106100
1.87-1.963.60.1066.1750320760.106100
1.96-2.053.60.0976.4738020390.097100
2.05-2.163.60.0817.6685318970.081100
2.16-2.293.60.0798.1663718360.079100
2.29-2.453.60.0827.4622217170.082100
2.45-2.653.60.0946.2566215870.094100
2.65-2.93.50.0885.1534015060.088100
2.9-3.243.50.0777.1472013300.077100
3.24-3.743.50.0726.4427512090.072100
3.74-4.593.50.0785.6364110340.07899.9
4.59-6.483.40.085527458080.08599.4
6.48-27.3383.10.0964.614744720.09696.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.45→27.338 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.094 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066
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. POLYETHYLENE GLYCOL MOLECULES FROM THE CRYSTALLIZATION CONDITIONS WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1851 5 %RANDOM
Rwork0.163 ---
obs0.164 37039 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.878 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.64 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.45→27.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 21 203 1820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221779
X-RAY DIFFRACTIONr_bond_other_d0.0010.021211
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9562414
X-RAY DIFFRACTIONr_angle_other_deg0.97332953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4815232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.00723.86775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9931511
X-RAY DIFFRACTIONr_chiral_restr0.1020.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022038
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02373
X-RAY DIFFRACTIONr_nbd_refined0.2210.2366
X-RAY DIFFRACTIONr_nbd_other0.1960.21255
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2878
X-RAY DIFFRACTIONr_nbtor_other0.0860.2895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.222
X-RAY DIFFRACTIONr_mcbond_it1.84731191
X-RAY DIFFRACTIONr_mcbond_other0.4783453
X-RAY DIFFRACTIONr_mcangle_it2.41551795
X-RAY DIFFRACTIONr_scbond_it3.7917752
X-RAY DIFFRACTIONr_scangle_it4.919619
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 127 -
Rwork0.196 2548 -
all-2675 -
obs--99.78 %
Refinement TLS params.Method: refined / Origin x: 29.5682 Å / Origin y: 26.739 Å / Origin z: 13.5602 Å
111213212223313233
T-0.0013 Å2-0.0016 Å20.0182 Å2--0.0114 Å20.001 Å2---0.016 Å2
L0.2299 °20.1697 °2-0.0316 °2-0.464 °2-0.1047 °2--0.1473 °2
S-0.0213 Å °-0.0236 Å °-0.0248 Å °-0.1118 Å °0.0053 Å °-0.0359 Å °-0.0081 Å °0.0068 Å °0.0161 Å °

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