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- PDB-4peu: Structure of the polysaccharide lyase-like protein Cthe_2159 from... -

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Basic information

Entry
Database: PDB / ID: 4peu
TitleStructure of the polysaccharide lyase-like protein Cthe_2159 from C. thermocellum, native form with Calcium bound
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Beta-helix / Polysaccharide lyase / carbohydrate-binding / calcium-binding
Function / homologygalacturonan binding / xylan binding / Carbohydrate-binding domain-containing protein Cthe_2159 / Carbohydrate-binding domain-containing protein Cthe_2159 / cellulose binding / Prokaryotic membrane lipoprotein lipid attachment site profile. / calcium ion binding / plasma membrane / Carbohydrate-binding domain-containing protein Cthe_2159
Function and homology information
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8001 Å
AuthorsClose, D.W. / D'Angelo, S. / Bradbury, A.R.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A new family of beta-helix proteins with similarities to the polysaccharide lyases.
Authors: Close, D.W. / D'Angelo, S. / Bradbury, A.R.
History
DepositionApr 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.4Dec 27, 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_struct_conn_angle / refine_hist / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9804
Polymers32,8601
Non-polymers1203
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.6997, 123.429, 34.5297
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 32859.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2159 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A3DHD2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 19% PEG 8000, 0.1M MES pH 6.0, and 0.1M Calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→26.8 Å / Num. all: 55471 / Num. obs: 28069 / % possible obs: 97.2 % / Redundancy: 2 % / Biso Wilson estimate: 13.0353170306 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 17.16

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Processing

Software
NameVersionClassification
PHENIX1.9_1685refinement
HKL-3000data collection
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8001→26.8 Å / SU ML: 0.160898015246 / Cross valid method: FREE R-VALUE / σ(F): 1.33785346198 / Phase error: 16.4836141761
RfactorNum. reflection% reflectionSelection details
Rfree0.171032934604 5250 10.0183192123 %Random
Rwork0.145936557685 47154 --
obs0.148521419908 28069 96.9026794135 %-
all-52463 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.3067167183 Å2
Refinement stepCycle: LAST / Resolution: 1.8001→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 3 403 2270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00570206376421889
X-RAY DIFFRACTIONf_angle_d1.077869611372556
X-RAY DIFFRACTIONf_chiral_restr0.041042995236299
X-RAY DIFFRACTIONf_plane_restr0.00376660566506341
X-RAY DIFFRACTIONf_dihedral_angle_d12.4302642727695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.82050.2051933909481370.2134638994041105X-RAY DIFFRACTION68.2417582418
1.8205-1.84190.2401094017671460.1959801920821193X-RAY DIFFRACTION77.2648586267
1.8419-1.86440.2255735286041390.1897995116781409X-RAY DIFFRACTION84.5901639344
1.8644-1.8880.2153880718841590.1797100690241485X-RAY DIFFRACTION90.4788112273
1.888-1.91280.209854871691750.1753455144491518X-RAY DIFFRACTION91.5630070308
1.9128-1.9390.1996798378831630.1577650847851543X-RAY DIFFRACTION97.8211009174
1.939-1.96670.1797173129991960.1555406762681626X-RAY DIFFRACTION99.7809419496
1.9667-1.9960.1686247928731750.1505879060121603X-RAY DIFFRACTION99.9437886453
1.996-2.02720.197074586771950.1454424030311662X-RAY DIFFRACTION100
2.0272-2.06040.1632510943091760.1468082663021600X-RAY DIFFRACTION100
2.0604-2.0960.2112448418751630.1397052471791607X-RAY DIFFRACTION99.9435347261
2.096-2.13410.1656293591832030.1559470374671609X-RAY DIFFRACTION99.944842802
2.1341-2.17510.1996371724171740.1509326251341634X-RAY DIFFRACTION99.8895027624
2.1751-2.21950.1815089923341710.1498895625241602X-RAY DIFFRACTION99.606741573
2.2195-2.26770.1769706093331900.1610125902691598X-RAY DIFFRACTION99.6100278552
2.2677-2.32040.1730233350581760.1488365729011666X-RAY DIFFRACTION99.7292907417
2.3204-2.37840.1886129464681750.1321303342611609X-RAY DIFFRACTION99.943977591
2.3784-2.44270.1500849753641840.1394916563111634X-RAY DIFFRACTION100
2.4427-2.51450.1965943140691780.141937373461609X-RAY DIFFRACTION99.9440715884
2.5145-2.59560.1889323162421750.1408680676011614X-RAY DIFFRACTION99.9441340782
2.5956-2.68830.1313853859651830.138795475821639X-RAY DIFFRACTION99.8356164384
2.6883-2.79580.1598685405451790.1428604566841624X-RAY DIFFRACTION100
2.7958-2.92290.1713399713711820.1486438923841630X-RAY DIFFRACTION100
2.9229-3.07680.1794032070231790.1418844006951608X-RAY DIFFRACTION99.9440715884
3.0768-3.26930.1717157962311750.1412389102621617X-RAY DIFFRACTION100
3.2693-3.52120.1454750407991770.1282589293931646X-RAY DIFFRACTION100
3.5212-3.87460.1338933822441780.1216517482511614X-RAY DIFFRACTION99.7772828508
3.8746-4.43310.1475869394771800.130739795321626X-RAY DIFFRACTION100
4.4331-5.57690.1362601330741870.1363612650151596X-RAY DIFFRACTION99.7203579418
5.5769-26.81540.2207934436371800.182175054981628X-RAY DIFFRACTION99.6692392503
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)
11.406349085980.131432711628-0.4225943458672.323713122780.1266442957512.250376176720.0295833752443-0.01437463378190.172260459461-0.1008101923660.0706109304484-0.11333540974-0.1368576704780.140555407209-0.06621148161910.0748245187609-0.00316837061923-0.001431398981960.04968406028-0.006489876465870.098368297238941.354956763652.180684052810.4927336376
22.31166452336-0.1790454648460.7303034060840.833414928655-0.1134583525182.25088378958-0.04238782977-0.0167028930003-0.05254499793510.01392915186740.0330071410972-0.05591284181150.0230963369958-0.008022404128710.02467294325730.06823340330170.01497103523440.00517231596760.0144232418336-0.01100365634340.089658591772140.179520737139.37557408058.17542709984
33.17826107884-0.62849372301-0.1421877178551.273870048770.1261460023190.880490964802-0.04958033357810.0332047376884-0.175779629215-0.01240349143090.0088791717950.03786065827510.08147378258320.003587686611260.02932517703410.08622730936060.01114749063120.003589691576930.0477267453151-0.008453271786180.10231947330748.761432480224.58984143056.83838229461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 121 )
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 190 )
3X-RAY DIFFRACTION3chain 'A' and (resid 191 through 285 )

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