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- PDB-4jcw: Crystal structure of Clavibacter michiganensis expansin in comple... -

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Basic information

Entry
Database: PDB / ID: 4jcw
TitleCrystal structure of Clavibacter michiganensis expansin in complex with cellopentaose
Componentscellulose binding protein
KeywordsSUGAR BINDING PROTEIN / Carbohydrate binding module / cell wall loosening / Cell wall / Cellulose binding protein
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-cellopentaose / cellulase
Similarity search - Component
Biological speciesClavibacter michiganensis subsp. michiganensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYennawar, N.H. / Yennawar, H.P. / Georgelis, N. / Cosgrove, D.J.
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.J.
History
DepositionFeb 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Derived calculations
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
B: cellulose binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4143
Polymers43,5852
Non-polymers8291
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.936, 43.212, 64.300
Angle α, β, γ (deg.)88.75, 81.29, 82.70
Int Tables number1
Space group name H-MP1

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Components

#1: Protein cellulose binding protein


Mass: 21792.594 Da / Num. of mol.: 2 / Fragment: unp residues 546-746
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 / beta-cellopentaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.05M Ammonium Sulfate, 0.1M Sodium citrate, 15% PEG8000 , pH 7.3, 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: Apr 11, 2012
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: 1.75→75 Å / Num. all: 34991 / Num. obs: 33239 / % possible obs: 91.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.074
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
1.75-1.780.141179.5
1.78-1.810.125179.8
1.81-1.850.113182
1.85-1.890.115185.7
1.89-1.930.099186.8
1.93-1.970.089189.5
1.97-2.020.082191.3
2.02-2.070.093193.5
2.07-2.140.093196.1
2.14-2.20.099197.3
2.2-2.280.122195.6
2.28-2.380.12196.7
2.38-2.480.09198
2.48-2.610.114196.8
2.61-2.780.082198.8
2.78-2.990.083199.2
2.99-3.290.077195.2
3.29-3.770.059186.3
3.77-4.750.049184.5
4.75-1750.055192.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D30

3d30


Resolution: 1.75→22.928 Å / SU ML: 0.2 / σ(F): 0.04 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1890 5.69 %RANDOM
Rwork0.1726 ---
obs0.1757 33223 86.3 %-
all-34991 --
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→22.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 56 416 3536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073301
X-RAY DIFFRACTIONf_angle_d1.2014521
X-RAY DIFFRACTIONf_dihedral_angle_d11.8911245
X-RAY DIFFRACTIONf_chiral_restr0.072525
X-RAY DIFFRACTIONf_plane_restr0.005576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7464-1.79360.32271150.22191814X-RAY DIFFRACTION64
1.7936-1.84630.26411080.18931963X-RAY DIFFRACTION71
1.8463-1.90590.24271190.18412033X-RAY DIFFRACTION73
1.9059-1.9740.21441460.18072327X-RAY DIFFRACTION83
1.974-2.0530.24961500.18572496X-RAY DIFFRACTION90
2.053-2.14630.25121600.18382624X-RAY DIFFRACTION94
2.1463-2.25940.25571580.18372642X-RAY DIFFRACTION94
2.2594-2.40080.25381590.19472612X-RAY DIFFRACTION93
2.4008-2.58590.24471580.18922581X-RAY DIFFRACTION93
2.5859-2.84570.22811600.17672677X-RAY DIFFRACTION96
2.8457-3.25650.22891620.17322666X-RAY DIFFRACTION95
3.2565-4.09910.20831460.14772410X-RAY DIFFRACTION87
4.0991-22.92970.17011490.14992488X-RAY DIFFRACTION89
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)
12.0635-7.94127.86972.05072.01522.0247-0.67370.94331.2490.3734-0.0619-1.4019-1.3011.30890.98960.3362-0.1109-0.02590.3570.07280.4212-1.240630.1993-7.3757
29.2449-1.8778-2.71884.7569-3.96415.4578-0.04250.6667-0.3985-0.4809-0.00080.9997-0.0796-0.5780.00850.16060.0502-0.0320.2259-0.0060.1985-16.457924.3234-19.0173
39.4764-1.2744-6.83116.94130.95396.3741-0.1205-0.3139-0.46170.2974-0.15770.38610.3668-0.00560.27650.1681-0.00660.00350.1638-0.02650.1303-13.137912.5414-21.5728
42.1317.553-9.21688.6108-6.97442.1865-0.01140.4634-0.04950.13670.17390.1254-0.214-0.218-0.29220.2014-0.0615-0.00560.2874-0.00560.128-9.2121.6262-16.5978
58.8274-3.4672-6.55183.06012.89457.5448-0.179-0.11560.06130.17640.09310.05670.0539-0.03460.10910.17970.016-0.04060.11330.00570.096-6.502420.3761-10.719
67.84513.9917-2.52854.4716-0.04472.87660.10920.19450.4091-0.16640.06750.0651-0.2244-0.0904-0.18260.19560.0287-0.0120.13530.01480.1267-8.641426.1117-17.6211
75.2881-0.44520.65832.048-7.99777.649-0.1313-0.17440.69020.62220.67630.4598-0.6912-0.9332-0.43160.30750.09880.03030.25890.00590.2741-18.720831.3203-10.4138
80.02510.22940.18174.61872.83093.71450.0079-0.04320.00550.3318-0.01680.02880.13280.00350.01930.0708-0.01730.00970.1556-0.00020.1103-4.951313.4513-11.529
93.98970.84330.6035.55745.13342.07440.1650.55770.0209-0.404-0.2558-0.08860.2058-0.48430.14420.25160.0803-0.01580.22020.02620.1413-2.38642.4447-28.8061
102.3491-7.8449-7.68762.36228.48849.3187-0.3149-0.2704-0.35640.25250.0919-0.03330.31380.4314-0.24690.27070.00810.05850.2613-0.06250.34646.51094.8505-18.7588
117.69311.98616.99852.0124-9.53788.34210.72670.7794-0.67-1.036-0.7656-1.32010.95460.492-0.07830.32050.07120.06460.219-0.04090.427712.1883-2.8322-24.5474
126.0003-2.7708-1.11648.37361.43855.54640.11990.2637-0.414-0.2217-0.267-0.07880.59430.04090.1520.20120.01330.00550.18750.00740.10912.39714.4446-29.0735
138.63677.36156.1342.19528.86657.30220.2036-0.1715-0.45070.22650.0966-0.31060.24590.0015-0.36240.3250.0644-0.05750.14460.01560.16135.22441.6262-14.9485
146.0895-5.137-1.14264.89063.00277.7227-0.2269-0.1213-0.71240.15570.06020.20110.5506-0.16070.29010.267-0.04910.03810.11950.01020.2256-7.1623-3.7151-25.2749
156.36844.35132.4677.78128.66112.0429-0.31820.04350.108-0.16690.1750.31690.04980.08770.24210.28350.0046-0.01420.16280.05910.1364-3.36381.0035-7.3289
168.95724.3244-6.42072.4604-7.27169.52390.44770.24560.14880.26340.02530.4667-0.33340.2042-0.03190.30420.0227-0.01760.1206-0.06040.14513.19843.4253-53.6151
179.39290.8696-0.04715.734-1.81227.3633-0.3078-0.0514-0.6218-0.2670.1280.10870.5987-0.56580.12740.1714-0.02040.03470.1521-0.02630.1494-10.32985.4794-39.6731
189.6278-5.8907-7.69969.3056.84439.1344-0.28730.5066-0.73610.1202-0.17150.78080.6653-0.70250.40180.2118-0.0578-0.02450.20220.00470.2225-11.27920.9288-47.5465
192.4294-0.02360.66454.80332.78955.3520.06850.1014-0.1669-0.1507-0.08320.01580.12630.07860.01220.12370.02630.01150.11940.01350.0904-2.06748.1412-53.3903
206.27185.62487.86329.35387.80912.07640.1514-0.2551-0.012-0.3496-0.1952-0.1185-0.2442-0.37390.18140.15330.00320.03710.1650.00670.0857-5.41697.2479-49.7152
218.22716.9432.21476.69280.82562.50830.3195-0.10840.00050.2422-0.2190.02580.23610.0776-0.08350.20010.05470.02140.1368-0.02490.14633.11873.3254-49.1382
222.0194-2.37032.65372.33570.67784.44010.36350.1262-1.2003-0.2802-0.19670.16560.79960.2768-0.11440.41340.0754-0.05410.1674-0.02910.35732.0882-7.8098-54.0024
235.7475-3.4618-1.80812.71080.7052.1530.18190.2949-0.0041-0.2269-0.14160.00960.0731-0.0080.01740.18040.0042-0.02520.1278-0.02650.0828-7.744810.0534-57.5653
241.8260.385-0.3821.63810.04437.5626-0.0225-0.23690.08910.21650.08390.0366-0.4174-0.4332-0.07930.15330.0614-0.01270.1391-0.00680.1241-14.640218.7022-38.8748
252.08672.0329-8.91262.05788.70432.07890.49340.07940.9727-0.6087-0.0715-0.3888-0.8568-0.2488-0.28290.44610.1758-0.02040.33750.04940.2102-14.659328.8624-44.7295
262.0522-9.3863.99462.0267-2.87735.661-0.9351-0.37020.97850.89870.5996-0.5559-0.8097-0.4360.14050.32530.0485-0.00810.18030.0370.4599-16.505134.3265-41.741
278.2379-2.0579-6.96057.28085.4729.17890.20960.07270.45370.2006-0.1352-0.1365-0.641-0.4628-0.12130.22650.0438-0.03460.16090.00390.1013-10.202223.2574-37.1196
282.0537-0.0326-4.10376.97244.01972.0269-0.1931-1.13720.92390.98380.12790.2628-0.0099-0.15250.07180.32550.12810.00910.5209-0.04810.2959-22.953427.8007-39.4267
297.8884-1.3341-5.65023.6825-0.07588.07710.12670.22030.4093-0.07570.08050.0639-0.354-0.5645-0.16990.13860.0008-0.03810.1334-0.00110.1151-17.715823.9141-50.0703
303.3147-0.0565-0.86821.301-1.30092.08520.022-0.0736-0.0959-0.04420.08860.08220.1141-0.3305-0.10360.1634-0.004-0.01180.14830.00860.1709-21.944816.1092-49.1073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:6)
2X-RAY DIFFRACTION2(chain A and resid 7:14)
3X-RAY DIFFRACTION3(chain A and resid 15:31)
4X-RAY DIFFRACTION4(chain A and resid 32:40)
5X-RAY DIFFRACTION5(chain A and resid 41:64)
6X-RAY DIFFRACTION6(chain A and resid 65:83)
7X-RAY DIFFRACTION7(chain A and resid 84:94)
8X-RAY DIFFRACTION8(chain A and resid 95:115)
9X-RAY DIFFRACTION9(chain A and resid 116:130)
10X-RAY DIFFRACTION10(chain A and resid 131:141)
11X-RAY DIFFRACTION11(chain A and resid 142:148)
12X-RAY DIFFRACTION12(chain A and resid 149:166)
13X-RAY DIFFRACTION13(chain A and resid 167:182)
14X-RAY DIFFRACTION14(chain A and resid 183:192)
15X-RAY DIFFRACTION15(chain A and resid 193:202)
16X-RAY DIFFRACTION16(chain B and resid 1:12)
17X-RAY DIFFRACTION17(chain B and resid 13:25)
18X-RAY DIFFRACTION18(chain B and resid 26:34)
19X-RAY DIFFRACTION19(chain B and resid 35:61)
20X-RAY DIFFRACTION20(chain B and resid 62:68)
21X-RAY DIFFRACTION21(chain B and resid 69:83)
22X-RAY DIFFRACTION22(chain B and resid 84:94)
23X-RAY DIFFRACTION23(chain B and resid 95:111)
24X-RAY DIFFRACTION24(chain B and resid 112:133)
25X-RAY DIFFRACTION25(chain B and resid 134:142)
26X-RAY DIFFRACTION26(chain B and resid 143:148)
27X-RAY DIFFRACTION27(chain B and resid 149:163)
28X-RAY DIFFRACTION28(chain B and resid 164:170)
29X-RAY DIFFRACTION29(chain B and resid 171:185)
30X-RAY DIFFRACTION30(chain B and resid 186:202)

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