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

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Basic information

Entry
Database: PDB / ID: 3mmu
TitleCrystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima
ComponentsEndoglucanaseCellulase
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
: / NICKEL (II) ION / Endoglucanase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsPereira, J.H. / Chen, Z. / McAndrew, R.P. / Sapra, R. / Chhabra, S.R. / Sale, K.L. / Simmons, B.A. / Adams, P.D.
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
E: Endoglucanase
F: Endoglucanase
G: Endoglucanase
H: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,86964
Polymers299,5088
Non-polymers4,36156
Water21,6001199
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,12810
Polymers37,4391
Non-polymers6899
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9578
Polymers37,4391
Non-polymers5187
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,12810
Polymers37,4391
Non-polymers6899
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8396
Polymers37,4391
Non-polymers4015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0118
Polymers37,4391
Non-polymers5727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8987
Polymers37,4391
Non-polymers4606
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0118
Polymers37,4391
Non-polymers5727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8987
Polymers37,4391
Non-polymers4606
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Endoglucanase
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,08518
Polymers74,8772
Non-polymers1,20816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-81 kcal/mol
Surface area24410 Å2
MethodPISA
10
C: Endoglucanase
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,96716
Polymers74,8772
Non-polymers1,09014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-78 kcal/mol
Surface area24540 Å2
MethodPISA
11
E: Endoglucanase
F: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,90915
Polymers74,8772
Non-polymers1,03213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-84 kcal/mol
Surface area24380 Å2
MethodPISA
12
G: Endoglucanase
H: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,90915
Polymers74,8772
Non-polymers1,03213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-84 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.584, 95.791, 103.497
Angle α, β, γ (deg.)64.08, 75.07, 68.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Endoglucanase / Cellulase / Endoglucanase Cel5A


Mass: 37438.523 Da / Num. of mol.: 8
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.: 20 / Source method: obtained synthetically / Formula: Cd
#3: Chemical...
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1199 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.02 M Nickel(II) chloride, 0.02 M Magnesium chloride, 0.02 M Cadmium chloride, 0.1 M Sodium acetate trihydrate pH 4.5 and 16 % of Polyethylene glycol monomethyl ether 2000, VAPOR DIFFUSION, ...Details: 0.02 M Nickel(II) chloride, 0.02 M Magnesium chloride, 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: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 133326 / Num. obs: 125889 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.28 Å / % possible all: 74.1

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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: 1CEN

1cen


Resolution: 2.201→46.987 Å / SU ML: 2.19 / σ(F): 0.16 / Phase error: 23.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 6299 5 %RANDOM
Rwork0.2051 ---
obs0.2058 125889 88.73 %-
all-133326 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.68 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.408 Å28.572 Å23.769 Å2
2---1.356 Å2-0.482 Å2
3----1.598 Å2
Refinement stepCycle: LAST / Resolution: 2.201→46.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20816 0 56 1199 22071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01321464
X-RAY DIFFRACTIONf_angle_d1.25829040
X-RAY DIFFRACTIONf_dihedral_angle_d17.3827800
X-RAY DIFFRACTIONf_chiral_restr0.0782912
X-RAY DIFFRACTIONf_plane_restr0.0053688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2011-2.22610.31310.27322440X-RAY DIFFRACTION55
2.2261-2.25230.28641760.28583069X-RAY DIFFRACTION67
2.2523-2.27980.28411420.26912968X-RAY DIFFRACTION67
2.2798-2.30870.2941650.25913236X-RAY DIFFRACTION71
2.3087-2.3390.28511730.2553258X-RAY DIFFRACTION73
2.339-2.37110.28111900.25873483X-RAY DIFFRACTION77
2.3711-2.4050.27541810.25933682X-RAY DIFFRACTION81
2.405-2.44090.26792090.24923708X-RAY DIFFRACTION84
2.4409-2.4790.26011890.2383955X-RAY DIFFRACTION87
2.479-2.51960.24421820.2384012X-RAY DIFFRACTION88
2.5196-2.56310.26892270.23853978X-RAY DIFFRACTION89
2.5631-2.60970.23461980.23544061X-RAY DIFFRACTION91
2.6097-2.65990.2612380.22464178X-RAY DIFFRACTION92
2.6599-2.71420.24942540.22594103X-RAY DIFFRACTION93
2.7142-2.77320.25871930.23984113X-RAY DIFFRACTION93
2.7732-2.83770.26492300.23214211X-RAY DIFFRACTION94
2.8377-2.90860.22542140.22554285X-RAY DIFFRACTION94
2.9086-2.98720.24732460.22064236X-RAY DIFFRACTION95
2.9872-3.07510.22662310.22644254X-RAY DIFFRACTION95
3.0751-3.17440.23282480.21484288X-RAY DIFFRACTION96
3.1744-3.28780.21952060.21094367X-RAY DIFFRACTION96
3.2878-3.41940.22652410.21254337X-RAY DIFFRACTION97
3.4194-3.5750.22172260.2054401X-RAY DIFFRACTION97
3.575-3.76340.20272550.19444343X-RAY DIFFRACTION98
3.7634-3.9990.18762000.18494465X-RAY DIFFRACTION98
3.999-4.30760.16992130.16954415X-RAY DIFFRACTION98
4.3076-4.74070.16072140.15994425X-RAY DIFFRACTION98
4.7407-5.42590.16462170.16344449X-RAY DIFFRACTION99
5.4259-6.83270.20932570.18734440X-RAY DIFFRACTION99
6.8327-46.99720.19022530.18394430X-RAY DIFFRACTION99
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)
10.82430.0455-0.17211.0389-0.0161.5950.04150.27050.1251-0.1431-0.1037-0.09650.02790.05540.07450.15520.02340.00370.30410.02530.205444.711823.594329.6908
21.215-0.4067-0.50561.60650.23671.3181-0.07410.1526-0.36050.2543-0.05680.33860.2064-0.06340.12960.2077-0.02350.00890.1653-0.07170.363135.0927-3.621447.6105
31.8647-0.34620.11841.4398-0.20891.5852-0.0342-0.4976-0.06110.33240.0937-0.05920.36460.1595-0.05020.47960.0138-0.07330.37910.00480.208549.897721.89390.5254
41.2988-0.28780.56110.6007-0.36431.8874-0.1802-0.0770.45150.30280.02040.0379-0.52910.09330.16210.3862-0.1196-0.07840.1727-0.06780.383749.450150.949872.6735
51.1109-0.5146-0.6741.5750.78361.2838-0.2479-0.36140.12430.29520.2844-0.09890.18280.29-0.05120.3530.0969-0.0140.3865-0.03730.21168.078836.285493.4942
60.9645-0.5411-0.45391.45210.43091.6142-0.3734-0.1536-0.33750.45530.19660.19610.58890.0250.17850.49820.02550.16670.19010.07560.29875.05975.339280.0302
71.4981-0.06470.09761.2109-0.09591.14390.05560.3748-0.1594-0.136-0.03730.03040.0312-0.1885-0.01990.17020.0017-0.01850.3731-0.01790.22771.651626.840233.2944
81.0405-0.42430.48941.4403-0.11031.27480.07070.16320.28560.0347-0.1055-0.2641-0.2412-0.03460.02310.24050.03370.0540.19780.08690.317413.706956.032245.9909
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
5X-RAY DIFFRACTION5chain EE3 - 311
6X-RAY DIFFRACTION6chain FF3 - 311
7X-RAY DIFFRACTION7chain GG3 - 311
8X-RAY DIFFRACTION8chain HH3 - 311

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