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

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Basic information

Entry
Database: PDB / ID: 4phb
TitleStructure of the polysaccharide lyase-like protein Cthe_2159 from C. thermocellum, Gadolinium derivative
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Beta-helix / Polysaccharide lyase / carbohydrate-binding / Gadolinium
Function / homology
Function and homology information


galacturonan binding / xylan binding / cellulose binding / calcium ion binding / plasma membrane
Similarity search - Function
Carbohydrate-binding domain-containing protein Cthe_2159 / Carbohydrate-binding domain-containing protein Cthe_2159 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
GADOLINIUM ATOM / Carbohydrate-binding domain-containing protein Cthe_2159
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1781 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
DepositionMay 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_related ...entity_src_gen / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_related.content_type ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_related.content_type / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)34,74713
Polymers32,8601
Non-polymers1,88712
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.81, 122.84, 34.5099
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

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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-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Gd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.8 %
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: 2.178→34.51 Å / Num. obs: 15967 / % possible obs: 99.74 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.9104968048 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 7.98

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Processing

Software
NameVersionClassification
PHENIX1.9_1685refinement
HKL-30001.9_1685data collection
SCALA(phenix.refine: 1.9_1685)data scaling
RefinementResolution: 2.1781→34.5099 Å / SU ML: 0.250667241819 / Cross valid method: FREE R-VALUE / σ(F): 1.35725765718 / Phase error: 22.9639911101
RfactorNum. reflection% reflection
Rfree0.234066145504 2949 10.0391489362 %
Rwork0.184037073211 26426 -
obs0.189038191589 29375 99.3371884617 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.0779786559 Å2
Refinement stepCycle: LAST / Resolution: 2.1781→34.5099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 12 211 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008392013618251866
X-RAY DIFFRACTIONf_angle_d1.07653575992523
X-RAY DIFFRACTIONf_chiral_restr0.0430249892127296
X-RAY DIFFRACTIONf_plane_restr0.0037525915428335
X-RAY DIFFRACTIONf_dihedral_angle_d13.0145179693684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1781-2.21380.3395198499371370.2693156135971224X-RAY DIFFRACTION96.5933286018
2.2138-2.2520.3210742730731380.2582983228511243X-RAY DIFFRACTION99.7111913357
2.252-2.29290.2941152564111470.2440676404371304X-RAY DIFFRACTION99.7936726272
2.2929-2.3370.2769495435871410.2272367692771241X-RAY DIFFRACTION99.2103374013
2.337-2.38470.2736808419831390.228205919211239X-RAY DIFFRACTION99.7827661115
2.3847-2.43650.3364412060021430.2323878293111277X-RAY DIFFRACTION99.0928122819
2.4365-2.49320.2979283894471330.2303927568841254X-RAY DIFFRACTION97.8828510939
2.4932-2.55550.3054483920571410.2302474213931244X-RAY DIFFRACTION100
2.5555-2.62460.2603522043481390.2174116733271258X-RAY DIFFRACTION99.0780141844
2.6246-2.70180.3073148840231400.2018408325671244X-RAY DIFFRACTION98.5053380783
2.7018-2.7890.2233925209631360.1883345949281279X-RAY DIFFRACTION100
2.789-2.88860.2204315435621430.1930504498371270X-RAY DIFFRACTION99.1578947368
2.8886-3.00420.2441858238881410.1821188116661229X-RAY DIFFRACTION99.7815003642
3.0042-3.14080.2575053753611420.1702247500331289X-RAY DIFFRACTION99.2371705964
3.1408-3.30630.2059915212151330.1662157649011243X-RAY DIFFRACTION99.854862119
3.3063-3.51330.1994004710721440.1534131452481281X-RAY DIFFRACTION99.8598458304
3.5133-3.78420.186410683291440.1466270152291263X-RAY DIFFRACTION99.9289772727
3.7842-4.16450.2300930936291450.1478285270841250X-RAY DIFFRACTION100
4.1645-4.76570.1606244691791390.1321404320161261X-RAY DIFFRACTION99.3612491128
4.7657-5.99920.1953789309361400.1555770605441271X-RAY DIFFRACTION100
5.9992-34.51420.2094390161571440.210997672291262X-RAY DIFFRACTION99.3639575972
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)
17.052905870383.506625932171.797187169557.70406050867-2.231648550665.384817465790.3310024119050.5016678474060.690446330244-0.229243205820.0988500853511-0.122753309942-0.0113997832849-0.105106380041-0.316540883840.3666731612990.05673388314910.02195643915460.125467072480.03159743667370.2104584517130.556701132558.058286098217.759163635
25.31046881961-2.3352169649-0.8475936348162.859026618660.9487495291271.426086703460.0208378750333-0.1704830551620.5269721377420.1997418469840.093250814855-0.2004620698020.07094556731230.143092677776-0.1152417580460.264865131939-0.008078580488030.01687837367070.1024346202060.01624387744710.17295364471431.463535994952.996598330923.9367979351
33.761189714550.2124938558060.2928407705653.802610428990.3716655654122.016891357970.0796073821791-0.0484869675827-0.2010953531990.03909991709360.04462008725810.184228616929-0.2127515965940.000865514197922-0.1244216222580.217409965951-0.01650266979760.0357353323470.04808822074660.02278110408360.15943700991828.377395786547.609047639124.6230266781
43.155532058850.4994539604-2.292445984395.270583094741.530008418487.031861733640.1799533163020.1080277382990.30161888353-0.0180094092539-0.1302474232910.0693255493893-0.465581067592-0.658974429229-0.08287242145370.229429794010.04176043447070.01206300987880.1240985495840.02612681496130.15114589390523.279938470245.5279635727.3661493421
55.601320987370.7291950413152.693244154991.92209443825-0.1378121964883.530338323580.128807903131-0.214194829656-0.07562333344010.12660227448-0.0182760349493-0.06646839448370.05620942805960.0679958921815-0.07847273513640.2321381009630.0137724791040.005710800385570.07197171274660.007898812824340.14694439995934.939100692141.719622089729.0235407343
62.950499904180.717566975220.284940315721.446134449420.5559383251391.18168247876-0.04110416399560.09183667395530.039839521005-0.003540257358760.0735008422296-0.02202626443340.0433596841645-0.0732875167883-0.05215027970480.223442036905-0.000101003678840.005982061090420.1125478062430.03211447677140.11910057449426.664774805433.792618564724.2077648215
75.70913201728-2.10422560735-1.127978594294.77670775191.04777324760.377613718060.024154981679-0.6604134009240.520607684550.5113746300390.0991505803090.06898819369490.2271260310260.107166318256-0.10620883330.314844668334-0.03701801755570.02139916801080.187148103928-0.01440721077560.18360257889220.2278654228.370065177533.8491875998
85.875898793870.107298356314-1.093040946362.305935268710.07818490679931.6535480267-0.03262398103310.298742505915-0.165357135822-0.1280614415730.0441161496715-0.1867317363520.213954680453-0.09911900715780.01424971712670.362875213731-0.006484731265550.02675530839860.127917741562-0.01728528237390.1795567858423.608018441821.569080607925.1400489875
98.077582135051.29368872894-1.959269382885.659571279930.5816006953351.96337996264-0.249606426466-0.236468484885-0.4935284777730.00412757208506-0.0821002967046-0.6247759411390.6846373443280.1643464886510.1370084659040.446165438422-0.05055991644460.02293403320640.1174054445050.008739519407190.18744270824720.834111008916.347653019627.7062076217
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11(chain A and resid 37:56)37 - 5637 - 56
22(chain A and resid 57:85)57 - 8557 - 85
33(chain A and resid 86:108)86 - 10886 - 108
44(chain A and resid 109:121)109 - 121109 - 121
55(chain A and resid 122:153)122 - 153122 - 153
66(chain A and resid 154:212)154 - 212154 - 212
77(chain A and resid 213:235)213 - 235213 - 235
88(chain A and resid 236:263)236 - 263236 - 263
99(chain A and resid 264:284)264 - 284264 - 284

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