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- PDB-2aam: Crystal structure of a putative glycosidase (tm1410) from thermot... -

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Basic information

Entry
Database: PDB / ID: 2aam
TitleCrystal structure of a putative glycosidase (tm1410) from thermotoga maritima at 2.20 A resolution
ComponentsHypothetical protein TM1410
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Extracellular protein / Hypothetical protein TM1410-related / Glycoside-hydrolase family GH114, TIM-barrel domain / Glycoside-hydrolase family GH114 / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Uncharacterized protein TM_1410
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (tm1410) from THERMOTOGA MARITIMA at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein TM1410
B: Hypothetical protein TM1410
C: Hypothetical protein TM1410
D: Hypothetical protein TM1410
E: Hypothetical protein TM1410
F: Hypothetical protein TM1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,88649
Polymers219,4786
Non-polymers3,40743
Water16,682926
1
A: Hypothetical protein TM1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2249
Polymers36,5801
Non-polymers6458
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein TM1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,50112
Polymers36,5801
Non-polymers92111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical protein TM1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9486
Polymers36,5801
Non-polymers3685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hypothetical protein TM1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0407
Polymers36,5801
Non-polymers4606
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Hypothetical protein TM1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9486
Polymers36,5801
Non-polymers3685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Hypothetical protein TM1410
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2249
Polymers36,5801
Non-polymers6458
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)194.930, 84.620, 195.010
Angle α, β, γ (deg.)90.000, 119.900, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 30 - 310 / Label seq-ID: 16 - 296

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
Hypothetical protein TM1410


Mass: 36579.688 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm1410 / Plasmid: DL41 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1D0
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 6 / Source method: obtained synthetically
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 926 / Source method: isolated from a natural source / Formula: H2O
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: 6.43 Å3/Da / Density % sol: 80.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9.5
Details: 25.0% PEG-300, 10.0% Glycerol, 5.0% PEG-8000, 0.1M CHES pH 9.5 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979170, 0.918370
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2005 / Details: flat mirror
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979171
20.918371
ReflectionResolution: 2.2→28.59 Å / Num. obs: 263407 / % possible obs: 90.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.15
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID
2.2-2.2861.10.5431.9748264341381
2.28-2.3780.70.5432.3668338436971
2.37-2.4890.30.5433.0885227506001
2.48-2.6192.40.5433.784145501421
2.61-2.7794.10.5434.8184624506441
2.77-2.9895.40.5436.1985732516061
2.98-3.2896.60.5438.9488213534211
3.28-3.7697.30.54313.2188796542081
3.76-4.7297.60.54315.6186342531831
4.72-28.5996.50.54317.4486888537511

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
SHELXphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→28.59 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.963 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.13
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ELECTRON DENSITY IS DISORDERED AT THE N AND C-TERMINI, THEREFORE, THE STRUCTURE WAS NOT MODELED IN THESE REGIONS 3. ELECTRON DENSITY ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ELECTRON DENSITY IS DISORDERED AT THE N AND C-TERMINI, THEREFORE, THE STRUCTURE WAS NOT MODELED IN THESE REGIONS 3. ELECTRON DENSITY NEAR THE SIDECHAIN OF TYR 98 ON EACH SUBUNIT INDICATES A BOUND LIGAND. BASED ON STRUCTURAL HOMOLOGS, IT IS BELIEVED THAT THE UNKNOWN LIGAND CONTAINS A MODIFIED PYRANOSE RING.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 14007 5 %RANDOM
Rwork0.216 ---
all0.217 ---
obs-263407 99.39 %-
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: 37.156 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---1.13 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14182 0 324 926 15432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02214926
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212962
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.96320215
X-RAY DIFFRACTIONr_angle_other_deg0.983330229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68151711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17824.615806
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.906152428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3371588
X-RAY DIFFRACTIONr_chiral_restr0.0950.22058
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216465
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023155
X-RAY DIFFRACTIONr_nbd_refined0.1960.33133
X-RAY DIFFRACTIONr_nbd_other0.1730.313811
X-RAY DIFFRACTIONr_nbtor_refined0.1870.57314
X-RAY DIFFRACTIONr_nbtor_other0.0860.57964
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.51607
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0780.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1790.376
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.516
X-RAY DIFFRACTIONr_mcbond_it0.98429347
X-RAY DIFFRACTIONr_mcbond_other0.29323473
X-RAY DIFFRACTIONr_mcangle_it1.289313854
X-RAY DIFFRACTIONr_scbond_it1.92747395
X-RAY DIFFRACTIONr_scangle_it2.66456361
Refine LS restraints NCS

Ens-ID: 1 / Number: 4262 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.40.5
2BMEDIUM POSITIONAL0.390.5
3CMEDIUM POSITIONAL0.430.5
4DMEDIUM POSITIONAL0.30.5
5EMEDIUM POSITIONAL0.30.5
6FMEDIUM POSITIONAL0.350.5
1AMEDIUM POSITIONAL0.340.5
1AMEDIUM THERMAL0.622
2BMEDIUM THERMAL0.642
3CMEDIUM THERMAL0.672
4DMEDIUM THERMAL0.442
5EMEDIUM THERMAL0.442
6FMEDIUM THERMAL0.662
1AMEDIUM THERMAL0.652
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 1021 -
Rwork0.257 18835 -
obs--96.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4385-0.0920.90221.53730.00161.5014-0.00990.0744-0.15330.16220.0069-0.370.10750.34020.003-0.22280.0131-0.0399-0.12350.01-0.1203-21.39223.8-21.83
23.2322-0.5271.15291.8602-0.03312.09840.0007-0.0245-0.0183-0.19520.0050.3777-0.0627-0.2572-0.0057-0.22130.0265-0.0503-0.1580.0227-0.123825.11323.20516.701
33.4825-0.0229-1.15131.8457-0.01611.71790.05580.16270.1912-0.2902-0.0053-0.3767-0.01280.0824-0.0505-0.1639-0.01270.1402-0.20150.0094-0.114272.10920.62512.642
42.36360.1317-1.17621.80960.10162.1473-0.0474-0.2623-0.16720.3287-0.03110.32210.163-0.07090.0785-0.1674-0.00550.1192-0.14480.0174-0.1435-65.97721.875-8.65
50.81440.24490.0461.99750.15963.12260.0304-0.1279-0.0490.46720.0368-0.07610.13090.0731-0.0672-0.08930.0195-0.0151-0.1976-0.0309-0.246552.16821.86255.221
61.0048-0.06990.39581.99990.02162.93580.01220.1725-0.0517-0.4074-0.00180.08730.0288-0.1222-0.0104-0.1303-0.0056-0.0024-0.17510.0138-0.261-54.98922.142-54.061
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA28 - 31214 - 298
22BB27 - 31313 - 299
33CC27 - 31213 - 298
44DD27 - 31213 - 298
55EE27 - 31313 - 299
66FF27 - 31213 - 298

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