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- PDB-1vkd: Crystal structure of a predicted glycosidase (tm1225) from thermo... -

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Basic information

Entry
Database: PDB / ID: 1vkd
TitleCrystal structure of a predicted glycosidase (tm1225) from thermotoga maritima msb8 at 2.10 A resolution
Componentsconserved hypothetical protein TM1225
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homologyMannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (TM1225) from Thermotoga maritima at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein TM1225
B: conserved hypothetical protein TM1225
C: conserved hypothetical protein TM1225
D: conserved hypothetical protein TM1225
E: conserved hypothetical protein TM1225
F: conserved hypothetical protein TM1225
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,2098
Polymers233,9656
Non-polymers2442
Water17,186954
1
A: conserved hypothetical protein TM1225
B: conserved hypothetical protein TM1225
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1103
Polymers77,9882
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-15 kcal/mol
Surface area25060 Å2
MethodPISA
2
C: conserved hypothetical protein TM1225
D: conserved hypothetical protein TM1225
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1103
Polymers77,9882
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-13 kcal/mol
Surface area24980 Å2
MethodPISA
3
E: conserved hypothetical protein TM1225
F: conserved hypothetical protein TM1225


Theoretical massNumber of molelcules
Total (without water)77,9882
Polymers77,9882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-13 kcal/mol
Surface area24800 Å2
MethodPISA
4
A: conserved hypothetical protein TM1225
B: conserved hypothetical protein TM1225
hetero molecules

E: conserved hypothetical protein TM1225
F: conserved hypothetical protein TM1225

C: conserved hypothetical protein TM1225
D: conserved hypothetical protein TM1225
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,2098
Polymers233,9656
Non-polymers2442
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+3/2,-y+1,z+1/21
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area18550 Å2
ΔGint-97 kcal/mol
Surface area62980 Å2
MethodPISA
5
D: conserved hypothetical protein TM1225
hetero molecules

F: conserved hypothetical protein TM1225

B: conserved hypothetical protein TM1225


Theoretical massNumber of molelcules
Total (without water)117,1044
Polymers116,9823
Non-polymers1221
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_745-x+2,y-1/2,-z+1/21
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area6070 Å2
ΔGint-27 kcal/mol
Surface area34530 Å2
MethodPISA
6
A: conserved hypothetical protein TM1225
hetero molecules

E: conserved hypothetical protein TM1225

C: conserved hypothetical protein TM1225


Theoretical massNumber of molelcules
Total (without water)117,1044
Polymers116,9823
Non-polymers1221
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+3/2,-y+1,z+1/21
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area6130 Å2
ΔGint-27 kcal/mol
Surface area34800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.867, 100.908, 253.433
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / Refine code: 2

Dom-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1MSEAA1 - 32613 - 338
2MSEBB1 - 32613 - 338
3MSECC1 - 32613 - 338
4MSEDD1 - 32613 - 338
5SEREE1 - 32513 - 337
6MSEFF1 - 32613 - 338

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Components

#1: Protein
conserved hypothetical protein TM1225


Mass: 38994.113 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1225 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0V2
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 954 / 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: 2.36 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: Cacodylate pH 6.5, 5% PEG-1000, 0.2M MgCl2 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115896, 0.979508, 0.979740, 1.019778
DetectorType: ADSC / Detector: CCD / Date: Feb 4, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.1158961
20.9795081
30.979741
41.0197781
ReflectionResolution: 2.098→100.91 Å / Num. obs: 119326 / % possible obs: 91.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 40.37 Å2 / Rsym value: 0.086 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 7509 / Rsym value: 0.521 / % possible all: 78.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
SHARPphasing
autoSHARPphasing
SOLOMONphasing
REFMAC5.2.0001refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→82.17 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.768 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.173
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: NULL
RfactorNum. reflection% reflectionSelection details
Rfree0.20404 6056 5.1 %RANDOM
Rwork0.16203 ---
obs0.16417 113119 91.28 %-
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: 32.363 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--1.62 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 2.1→82.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15853 0 16 954 16823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02216408
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.92122395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93351950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90523.158817
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.538152428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.25615108
X-RAY DIFFRACTIONr_chiral_restr0.0950.22292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213070
X-RAY DIFFRACTIONr_nbd_refined0.2070.27784
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.21221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.2244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.242
X-RAY DIFFRACTIONr_mcbond_it1.53239976
X-RAY DIFFRACTIONr_mcangle_it2.461515922
X-RAY DIFFRACTIONr_scbond_it4.5387478
X-RAY DIFFRACTIONr_scangle_it6.376116473
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1300tight positional0.050.05
2B1300tight positional0.050.05
3C1300tight positional0.040.05
4D1300tight positional0.060.05
5E1300tight positional0.040.05
6F1300tight positional0.060.05
1A1333medium positional0.380.5
2B1333medium positional0.390.5
3C1333medium positional0.360.5
4D1333medium positional0.340.5
5E1333medium positional0.370.5
6F1333medium positional0.40.5
1A1300tight thermal0.150.5
2B1300tight thermal0.170.5
3C1300tight thermal0.150.5
4D1300tight thermal0.180.5
5E1300tight thermal0.150.5
6F1300tight thermal0.20.5
1A1333medium thermal1.242
2B1333medium thermal1.292
3C1333medium thermal1.182
4D1333medium thermal1.312
5E1333medium thermal1.182
6F1333medium thermal1.422
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 408 5.18 %
Rwork0.24 7469 -
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)
10.7318-0.20550.12260.7955-0.0381.0470.03870.0490.1052-0.10970.0218-0.1347-0.23390.2178-0.06040.0372-0.13630.12430.0212-0.0013-0.026480.81235.4447144.7887
20.62240.06650.04961.1314-0.1481.08690.02770.04140.1021-0.11410.02790.111-0.2639-0.0881-0.05560.03360.02260.0256-0.14090.0325-0.047341.579840.1718152.8593
31.0444-0.296-0.04821.02080.18251.3078-0.0067-0.03530.19470.07890.1031-0.1733-0.17810.3217-0.0965-0.094-0.0668-0.03770.0019-0.03020.0144123.521855.851499.2371
40.61150.07190.18891.0176-0.14541.00820.0079-0.1030.0860.1858-0.00020.1632-0.0907-0.0792-0.0077-0.09230.01980.0458-0.1291-0.0042-0.052783.485252.1993100.2991
50.8309-0.02630.38791.0343-0.05911.37490.0149-0.1664-0.02670.12350.04230.20660.1903-0.4334-0.0572-0.0964-0.090.01950.10280.0448-0.014546.169277.796757.8806
60.57850.0711-0.23941.1234-0.42410.81690-0.11350.0310.12950.0106-0.1266-0.01890.0258-0.0106-0.0901-0.0106-0.0734-0.1376-0.0236-0.087285.930881.726562.2868
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 32613 - 338
22BB1 - 32613 - 338
33CC1 - 32613 - 338
44DD1 - 32613 - 338
55EE1 - 32513 - 337
66FF1 - 32613 - 338

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