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- PDB-3mmw: Crystal structure of endoglucanase Cel5A from the hyperthermophil... -

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Basic information

Entry
Database: PDB / ID: 3mmw
TitleCrystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima
ComponentsEndoglucanase
KeywordsHYDROLASE / TIM barrel fold
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPereira, J.H. / Chen, Z. / McAndrew, R.P. / Sapra, R. / Chhabra, S.R. / Sale, K.L.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima.
Authors: Pereira, J.H. / Chen, Z. / McAndrew, R.P. / Sapra, R. / Chhabra, S.R. / Sale, K.L. / Simmons, B.A. / Adams, P.D.
History
DepositionApr 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Endoglucanase
B: Endoglucanase
C: Endoglucanase
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,99115
Polymers149,7544
Non-polymers1,23711
Water18,3931021
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7764
Polymers37,4391
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6633
Polymers37,4391
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8885
Polymers37,4391
Non-polymers4504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6633
Polymers37,4391
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Endoglucanase
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4397
Polymers74,8772
Non-polymers5625
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-44 kcal/mol
Surface area24250 Å2
MethodPISA
6
C: Endoglucanase
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5528
Polymers74,8772
Non-polymers6746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-47 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.814, 81.407, 103.139
Angle α, β, γ (deg.)90.00, 114.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Endoglucanase / Endoglucanase Cel5A


Mass: 37438.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1751 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X273
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.02 M Cadmium chloride, 0.1 M Sodium acetate trihydrate pH 4.5 and 16 % of Polyethylene glycol monomethyl ether 2000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 4, 2009
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 110327 / Num. obs: 103734 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.85→1.88 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MMU

3mmu


Resolution: 1.85→46.952 Å / SU ML: 1.88 / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 5185 5 %RANDOM
Rwork0.1886 ---
obs0.19 103734 93.98 %-
all-103734 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.634 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.596 Å20 Å2-1.863 Å2
2--1.256 Å20 Å2
3----7.08 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10408 0 11 1021 11440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710732
X-RAY DIFFRACTIONf_angle_d0.93914520
X-RAY DIFFRACTIONf_dihedral_angle_d16.9323900
X-RAY DIFFRACTIONf_chiral_restr0.0731456
X-RAY DIFFRACTIONf_plane_restr0.0041844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8495-1.87060.31631160.26672710X-RAY DIFFRACTION79
1.8706-1.89260.3081480.27132853X-RAY DIFFRACTION82
1.8926-1.91560.33111440.25712868X-RAY DIFFRACTION82
1.9156-1.93990.34791430.2463019X-RAY DIFFRACTION86
1.9399-1.96540.27521690.2392985X-RAY DIFFRACTION86
1.9654-1.99230.27281770.233043X-RAY DIFFRACTION88
1.9923-2.02080.23351660.21533145X-RAY DIFFRACTION90
2.0208-2.0510.25131480.21073246X-RAY DIFFRACTION93
2.051-2.0830.25021570.20653224X-RAY DIFFRACTION93
2.083-2.11720.22491620.20133215X-RAY DIFFRACTION92
2.1172-2.15370.2312010.20073281X-RAY DIFFRACTION94
2.1537-2.19280.25961950.20093271X-RAY DIFFRACTION94
2.1928-2.2350.23231680.19983274X-RAY DIFFRACTION95
2.235-2.28060.22071740.19373267X-RAY DIFFRACTION95
2.2806-2.33020.24881650.19223345X-RAY DIFFRACTION95
2.3302-2.38440.24521920.19533327X-RAY DIFFRACTION95
2.3844-2.44410.23691850.1913341X-RAY DIFFRACTION96
2.4441-2.51010.21171670.18623374X-RAY DIFFRACTION97
2.5101-2.5840.22871970.17793394X-RAY DIFFRACTION97
2.584-2.66740.20991860.18493413X-RAY DIFFRACTION98
2.6674-2.76270.20781770.18793395X-RAY DIFFRACTION98
2.7627-2.87330.20492050.19343438X-RAY DIFFRACTION98
2.8733-3.00410.21681900.19083437X-RAY DIFFRACTION99
3.0041-3.16240.22791790.18883458X-RAY DIFFRACTION99
3.1624-3.36050.21111910.17963500X-RAY DIFFRACTION100
3.3605-3.61990.18161850.17223477X-RAY DIFFRACTION100
3.6199-3.9840.1761700.15663549X-RAY DIFFRACTION100
3.984-4.56010.16721520.15623562X-RAY DIFFRACTION100
4.5601-5.74360.1851800.16353552X-RAY DIFFRACTION100
5.7436-46.96750.18751960.19053586X-RAY DIFFRACTION100
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)
10.6638-0.06280.2660.4504-0.20032.0325-0.00910.02060.0382-0.04780.03070.01710.1979-0.18170.00220.14870.0112-0.01180.116-0.00310.1039-13.8605-1.3082-50.1819
20.58590.3456-0.00830.648-0.23020.9224-0.00130.0058-0.1289-0.1589-0.1026-0.24580.1510.3302-0.00060.17060.09420.05590.23820.05230.22917.7006-8.9884-40.8584
30.99570.0830.04440.6720.15961.11290.0852-0.07970.04320.0652-0.0255-0.03470.07980.12520.04660.065-0.0123-0.0080.04250.00020.07944.0767-0.98518.313
40.7823-0.0222-0.31060.63980.29351.04210.06080.109-0.0507-0.0226-0.09280.09650.017-0.30760.00190.0726-0.0132-0.01370.1698-0.01330.1384-28.6971-3.8872-0.4714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 311
2X-RAY DIFFRACTION2chain BB3 - 311
3X-RAY DIFFRACTION3chain CC3 - 311
4X-RAY DIFFRACTION4chain DD3 - 311

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