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- PDB-4l48: Crystal structure of d78n mutant clavibacter michiganensis expans... -

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Basic information

Entry
Database: PDB / ID: 4l48
TitleCrystal structure of d78n mutant clavibacter michiganensis expansin in complex with cellohexaose
Componentscellulose binding protein
KeywordsSUGAR BINDING PROTEIN / Cellulose binding protein / Cell wall loosening
Function / homology
Function and homology information


cellulase / polysaccharide binding / cellulase activity / carbohydrate metabolic process
Similarity search - Function
: / Expansin, cellulose-binding-like domain / Expansin C-terminal domain / Expansin, cellulose-binding-like domain / RlpA-like protein, double-psi beta-barrel domain / Expansin, cellulose-binding-like domain superfamily / Lytic transglycolase / RlpA-like domain / RlpA-like domain superfamily / Cellulose binding domain ...: / Expansin, cellulose-binding-like domain / Expansin C-terminal domain / Expansin, cellulose-binding-like domain / RlpA-like protein, double-psi beta-barrel domain / Expansin, cellulose-binding-like domain superfamily / Lytic transglycolase / RlpA-like domain / RlpA-like domain superfamily / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Barwin-like endoglucanases / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-cellohexaose / cellulase
Similarity search - Component
Biological speciesClavibacter michiganensis subsp. michiganensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYennawar, N.H. / Yennawar, H.P. / Georgelis, N. / Cosgrove, D.
CitationJournal: To be Published
Title: Crystal structure of wild type and d78n mutant clavibacter michiganensis expansin, in apo form and in complex with oligosaccharides
Authors: Yennawar, N.H. / Yennawar, H.P. / Georgelis, N. / Cosgrove, D.
History
DepositionJun 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Structure summary
Revision 1.2Oct 21, 2015Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cellulose binding protein
C: cellulose binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5654
Polymers43,5832
Non-polymers1,9822
Water11,998666
1
A: cellulose binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7822
Polymers21,7921
Non-polymers9911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: cellulose binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7822
Polymers21,7921
Non-polymers9911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.758, 34.555, 81.144
Angle α, β, γ (deg.)90.00, 95.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein cellulose binding protein


Mass: 21791.609 Da / Num. of mol.: 2 / Fragment: unp residues 546-746 / Mutation: d78n
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clavibacter michiganensis subsp. michiganensis (bacteria)
Strain: NCPPB 382 / Gene: celA, pCM1_0020 / Production host: Escherichia coli (E. coli) / References: UniProt: A5CLK3, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellohexaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 990.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellohexaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.5M KCl, 12% PEG 8000, 10% glycerol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 17, 2012 / Details: Varimax confocal optics
RadiationMonochromator: VARIMAX CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 21474 / Num. obs: 21474 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 14.25 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.09
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.142.20.1177.3193.5
2.14-2.180.113198.7
2.18-2.220.1051100
2.22-2.260.106199.6
2.26-2.310.1199.7
2.31-2.370.093199.8
2.37-2.420.092199.9
2.42-2.490.086199.6
2.49-2.560.086199.9
2.56-2.650.077199.9
2.65-2.740.071199.6
2.74-2.850.067199.9
2.85-2.980.06199.8
2.98-3.140.051199.5
3.14-3.330.05199.3
3.33-3.590.05199.1
3.59-3.950.047198.2
3.95-4.520.045197.4
4.52-5.70.045197.6
5.7-500.05193

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4JS7

4js7


Resolution: 2.1→22.371 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1971 9.32 %Random
Rwork0.1953 ---
all0.201 21474 --
obs0.201 21142 96.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→22.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 134 666 3862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023286
X-RAY DIFFRACTIONf_angle_d0.634498
X-RAY DIFFRACTIONf_dihedral_angle_d10.1291232
X-RAY DIFFRACTIONf_chiral_restr0.04532
X-RAY DIFFRACTIONf_plane_restr0.003566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0956-2.1480.29251250.20811213X-RAY DIFFRACTION86
2.148-2.2060.27461420.20481373X-RAY DIFFRACTION99
2.206-2.27090.30511430.21241382X-RAY DIFFRACTION98
2.2709-2.34410.31141420.21151349X-RAY DIFFRACTION98
2.3441-2.42780.28681370.21531378X-RAY DIFFRACTION98
2.4278-2.52490.29681390.21491352X-RAY DIFFRACTION97
2.5249-2.63960.31591420.21671380X-RAY DIFFRACTION98
2.6396-2.77850.26131400.21351351X-RAY DIFFRACTION98
2.7785-2.95220.27411420.21551391X-RAY DIFFRACTION98
2.9522-3.17960.24261430.19291390X-RAY DIFFRACTION98
3.1796-3.49850.2151450.18031410X-RAY DIFFRACTION99
3.4985-4.00220.26131420.16081384X-RAY DIFFRACTION98
4.0022-5.03290.19661440.17071398X-RAY DIFFRACTION96
5.0329-22.37260.22891450.20141420X-RAY DIFFRACTION95
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)
18.6719-5.80371.58018.91093.03349.0220.20710.4810.18790.07580.2235-0.13180.02221.0659-0.31620.0720.003-0.08920.379-0.07010.089832.312410.489737.0825
20.84721.31371.24032.16832.2574.6245-0.1236-0.03930.1277-0.2340.1996-0.20450.2463-0.5878-0.04270.04570.1144-0.00250.13240.00750.198112.72694.407330.1133
30.4082-0.05790.14030.6826-0.07210.93980.10590.0903-0.0809-0.0918-0.04720.06980.19630.0339-0.05370.16010.0055-0.05790.1447-0.01840.101120.96643.4624.22
41.3156-0.1406-0.43840.47550.38292.1642-0.3735-0.1424-0.16520.1797-0.42070.07720.3262-0.0070.3293-0.2408-0.04980.14590.3801-0.00540.101926.66941.296341.3363
51.1892-0.2509-0.60310.7045-0.20350.4919-0.07350.2073-0.0846-0.0289-0.01060.1697-0.1204-0.04160.08850.16850.001-0.02740.129-0.02520.0822.23967.448831.5853
65.92680.33653.3416.3539-1.21986.6859-0.3838-0.40070.69830.36160.27320.9652-0.3871-0.55580.13730.14260.0395-0.03070.1777-0.00670.260816.53842.167641.3958
71.4791-0.28940.46011.09790.21681.531-0.0452-0.3773-0.03550.10620.07440.12160.1308-0.28910.01410.21240.0545-0.0060.2197-0.02350.103321.17088.768643.2028
8-0.077-0.0859-0.05190.4670.3541.5192-0.0497-0.2743-0.09380.01630.0471-0.09170.0976-0.088-0.0180.08970.00580.00230.20490.00470.109528.5161-3.196521.2242
91.7373-0.2187-0.76461.6875-0.43710.71030.0010.11050.2343-0.16540.07580.10910.003-0.0953-0.04830.13190.0065-0.01340.13710.00210.108724.12981.49218.9143
103.2425-1.2885-1.714.39651.6067.89140.1112-0.07790.1882-0.6685-0.0056-0.49910.19741.0776-0.08840.31910.03650.03240.22030.01250.107334.3120.38711.1668
113.16040.40940.42541.8431-0.72122.31730.00980.07050.0668-0.17240.0602-0.073-0.2802-0.2415-0.0720.15930.0173-0.00510.08180.01120.110327.1165.48325.2054
124.29961.40453.93774.17051.81458.4851-0.13740.8211-0.1052-0.3220.16180.057-0.25020.2490.09550.1530.0396-0.03880.2528-0.0270.157730.5882-3.64614.0921
132.1355-0.014-0.04620.4593-0.57220.78460.03960.03120.1020.05310.07550.00970.02910.0607-0.13710.17060.0222-0.0180.1341-0.02980.12627.6834-5.65199.3946
149.15820.18252.41134.65311.34478.8769-0.0156-0.6548-1.13560.31810.2788-0.15430.96360.2513-0.16010.30920.09190.07160.189-0.00910.163332.7966-12.01418.0425
158.59653.70240.21537.69342.61555.62150.3114-0.0889-0.00950.1770.0436-0.43350.08920.0521-0.28470.2379-0.0298-0.03040.1113-0.02610.12963.0749-5.93813.8726
160.4848-0.0112-1.01942.84342.10684.6766-0.09910.20770.0568-0.0365-0.04410.4233-0.1817-0.36520.16850.1134-0.01810.0030.2029-0.01690.1622-17.13172.225412.8265
172.98381.3755-0.14028.7480.00313.44880.03880.23650.3884-0.53830.09720.0536-0.6584-0.3927-0.10620.21390.0335-0.01480.13090.04310.1678-12.3516.3057.9983
180.88170.5123-0.32041.39970.18361.39630.02980.02940.04590.1626-0.0223-0.05690.03070.1768-0.03160.08650.0142-0.0040.1242-0.01220.1038-3.99930.46969.881
192.7748-0.0677-0.65711.37420.74262.8337-0.13230.0787-0.09670.0612-0.00080.0699-0.0202-0.3950.13550.07470.00560.01770.1448-0.0220.0935-9.9419-4.72486.5886
203.10812.6065-0.59199.14932.88233.7172-0.05350.2293-0.0245-0.5253-0.15440.2628-0.4387-0.16440.18930.18040.0115-0.01280.1963-0.01580.1576-11.6086-0.2869-5.3985
210.8181-0.9069-0.98681.17991.58472.1405-0.0295-0.08850.0944-0.04450.0518-0.08920.05250.0871-0.04850.1152-0.0033-0.02010.06090.00950.1434-4.56835.843615.7665
223.0380.4107-1.71322.5124-1.60912.84230.237-0.59590.14650.3033-0.05790.3312-0.30760.5152-0.0870.181-0.0283-0.02170.1436-0.01590.1481-9.04463.699230.2599
233.4496-0.7392-1.15134.5007-1.99461.5170.263-0.19850.07830.7738-0.0164-0.2872-0.4840.0529-0.09960.251-0.0194-0.00510.13810.03910.116-2.56195.24342.1597
243.1521-0.8704-0.86622.6506-0.8853.3514-0.3335-0.0946-0.27550.35690.08470.12390.3870.03030.16830.11430.0197-0.00120.06120.01130.0888-9.5841-2.103629.8458
254.0021.85542.03877.00312.6345.50980.5541-0.70510.38921.3940.1540.3966-0.61120.1247-0.48830.3426-0.0680.13690.2141-0.07310.1994-12.53954.735744.0156
264.0327-2.3912-2.02472.6041.86592.5962-0.17530.174-0.05180.13120.02110.18380.3964-0.37190.14260.1093-0.0373-0.00790.14020.01510.1104-0.44598.946531.0728
272.5886-0.2888-1.35971.69540.76076.3417-0.1189-0.062-0.04050.0588-0.7032-0.1909-0.6358-0.2560.68870.1556-0.0096-0.03190.18090.02860.2639-16.140912.618432.0543
282.0162-1.4278-1.97225.96040.39554.42190.07870.62990.6676-0.1205-0.29810.186-0.346-0.15150.16930.2139-0.007-0.08330.2289-0.05420.1754-0.45716.728922.5946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:6)
2X-RAY DIFFRACTION2(chain A and resid 7:16)
3X-RAY DIFFRACTION3(chain A and resid 17:52)
4X-RAY DIFFRACTION4(chain A and resid 53:58)
5X-RAY DIFFRACTION5(chain A and resid 59:81)
6X-RAY DIFFRACTION6(chain A and resid 82:90)
7X-RAY DIFFRACTION7(chain A and resid 91:98)
8X-RAY DIFFRACTION8(chain A and resid 99:115)
9X-RAY DIFFRACTION9(chain A and resid 116:135)
10X-RAY DIFFRACTION10(chain A and resid 136:143)
11X-RAY DIFFRACTION11(chain A and resid 144:163)
12X-RAY DIFFRACTION12(chain A and resid 164:173)
13X-RAY DIFFRACTION13(chain A and resid 174:192)
14X-RAY DIFFRACTION14(chain A and resid 193:202)
15X-RAY DIFFRACTION15(chain C and resid 1:6)
16X-RAY DIFFRACTION16(chain C and resid 7:28)
17X-RAY DIFFRACTION17(chain C and resid 29:36)
18X-RAY DIFFRACTION18(chain C and resid 37:65)
19X-RAY DIFFRACTION19(chain C and resid 66:84)
20X-RAY DIFFRACTION20(chain C and resid 85:94)
21X-RAY DIFFRACTION21(chain C and resid 95:116)
22X-RAY DIFFRACTION22(chain C and resid 117:137)
23X-RAY DIFFRACTION23(chain C and resid 138:146)
24X-RAY DIFFRACTION24(chain C and resid 147:159)
25X-RAY DIFFRACTION25(chain C and resid 160:165)
26X-RAY DIFFRACTION26(chain C and resid 166:182)
27X-RAY DIFFRACTION27(chain C and resid 183:192)
28X-RAY DIFFRACTION28(chain C and resid 193:202)

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