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- PDB-2pbl: Crystal structure of a putative thioesterase (tm1040_2492) from s... -

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Basic information

Entry
Database: PDB / ID: 2pbl
TitleCrystal structure of a putative thioesterase (tm1040_2492) from silicibacter sp. tm1040 at 1.79 A resolution
ComponentsPutative esterase/lipase/thioesterase
KeywordsHYDROLASE / Alpha/beta-hydrolases fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Unknown ligand / Putative esterase/lipase/thioesterase
Similarity search - Component
Biological speciesSilicibacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.79 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative thioesterase (YP_614486.1) from Silicibacter sp. TM1040 at 1.79 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr1_auth_asym_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_asym_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_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 / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Putative esterase/lipase/thioesterase
B: Putative esterase/lipase/thioesterase
C: Putative esterase/lipase/thioesterase
D: Putative esterase/lipase/thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,46315
Polymers116,1074
Non-polymers35611
Water23,6001310
1
A: Putative esterase/lipase/thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0623
Polymers29,0271
Non-polymers352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative esterase/lipase/thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1815
Polymers29,0271
Non-polymers1554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative esterase/lipase/thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1574
Polymers29,0271
Non-polymers1303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative esterase/lipase/thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0623
Polymers29,0271
Non-polymers352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.197, 74.438, 95.727
Angle α, β, γ (deg.)90.000, 113.390, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASPASP3AA0 - 51 - 6
21GLYGLYASPASP3BB0 - 51 - 6
31GLYGLYASPASP3CC0 - 51 - 6
41GLYGLYASPASP3DD0 - 51 - 6
52ALAALAALAALA5AA6 - 2617 - 262
62ALAALAALAALA5BB6 - 2617 - 262
72ALAALAALAALA5CC6 - 2617 - 262
82ALAALAALAALA5DD6 - 2617 - 262

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative esterase/lipase/thioesterase


Mass: 29026.627 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter sp. (bacteria) / Strain: TM1040 / Gene: YP_614486.1, TM1040_2492 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GDP2

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Non-polymers , 5 types, 1321 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1310 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 43.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NANODROP, 0.2M MgCl2, 30.0% PEG 4000, 0.1M Tris-HCl pH 8.5, 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: 0.97937, 0.91837, 0.97910
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 10, 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
10.979371
20.918371
30.97911
ReflectionResolution: 1.79→29.45 Å / Num. obs: 93727 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.53 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.79-1.843.10.6531.12158069010.653100
1.84-1.893.10.5021.52120467580.502100
1.89-1.943.10.3981.82046065000.398100
1.94-23.20.3232.32011263840.323100
2-2.073.20.2642.81946961650.264100
2.07-2.143.20.223.21891459850.22100
2.14-2.223.20.23.51816557420.2100
2.22-2.313.20.1773.91753655350.177100
2.31-2.413.20.1484.71696053510.148100
2.41-2.533.20.1295.31614850990.129100
2.53-2.673.20.1195.51546048640.119100
2.67-2.833.20.1035.81451545740.103100
2.83-3.033.20.0955.71367843140.095100
3.03-3.273.20.0786.71275440190.078100
3.27-3.583.20.06481173237130.06499.9
3.58-43.20.0578.91059533550.05799.9
4-4.623.10.0578.9926129480.05799.8
4.62-5.663.10.0568.7791025170.05699.6
5.66-8.013.10.068.4605419410.0699.2
8.01-29.4530.0558.3318610620.05596.6

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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: 1.79→29.45 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.928 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.161
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. ONE MG ATOM AND FOUR CHLORIDE IONS FROM CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 5. ONE P-NITROBENZENE-LIKE UNKNOWN LIGAND IS MODELED NEAR TO HIS 135 IN EACH SUBUNIT. 6. PHOSPHATE IONS ARE MODELED IN THE UNKNOWN ELECTRON DENSITY NEAR GLU 149 IN EACH SUBUNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 4700 5 %RANDOM
Rwork0.221 ---
all0.224 ---
obs0.224 93699 99.86 %-
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: 17.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0.33 Å2
2---1.4 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.79→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8049 0 51 1310 9410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228402
X-RAY DIFFRACTIONr_bond_other_d0.0020.027547
X-RAY DIFFRACTIONr_angle_refined_deg1.711.9511482
X-RAY DIFFRACTIONr_angle_other_deg1.014317460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.27951066
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60923.777376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.28151249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3331553
X-RAY DIFFRACTIONr_chiral_restr0.10.21245
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029609
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021744
X-RAY DIFFRACTIONr_nbd_refined0.2120.31891
X-RAY DIFFRACTIONr_nbd_other0.1760.38188
X-RAY DIFFRACTIONr_nbtor_refined0.180.54253
X-RAY DIFFRACTIONr_nbtor_other0.0880.54656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.51650
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0310.51
X-RAY DIFFRACTIONr_metal_ion_refined0.1560.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.378
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.544
X-RAY DIFFRACTIONr_mcbond_it1.99735440
X-RAY DIFFRACTIONr_mcbond_other0.78932134
X-RAY DIFFRACTIONr_mcangle_it2.79358494
X-RAY DIFFRACTIONr_scbond_it5.29883454
X-RAY DIFFRACTIONr_scangle_it6.855112988
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A34TIGHT POSITIONAL0.030.05
2B34TIGHT POSITIONAL0.030.05
3C34TIGHT POSITIONAL0.030.05
4D34TIGHT POSITIONAL0.040.05
1A1485MEDIUM POSITIONAL0.170.5
2B1485MEDIUM POSITIONAL0.170.5
3C1485MEDIUM POSITIONAL0.190.5
4D1485MEDIUM POSITIONAL0.170.5
1A2287LOOSE POSITIONAL0.365
2B2287LOOSE POSITIONAL0.365
3C2287LOOSE POSITIONAL0.485
4D2287LOOSE POSITIONAL0.375
1A34TIGHT THERMAL0.150.5
2B34TIGHT THERMAL0.10.5
3C34TIGHT THERMAL0.10.5
4D34TIGHT THERMAL0.120.5
1A1485MEDIUM THERMAL1.22
2B1485MEDIUM THERMAL1.142
3C1485MEDIUM THERMAL1.182
4D1485MEDIUM THERMAL1.152
1A2287LOOSE THERMAL2.1710
2B2287LOOSE THERMAL2.2610
3C2287LOOSE THERMAL2.2110
4D2287LOOSE THERMAL2.2710
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 333 -
Rwork0.349 6562 -
obs-6895 99.94 %

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