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- PDB-4g68: Biochemical and structural insights into xylan utilization by the... -

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Basic information

Entry
Database: PDB / ID: 4g68
TitleBiochemical and structural insights into xylan utilization by the thermophilic bacteriumcaldanaerobius polysaccharolyticus
Components(ABC transporter) x 3
KeywordsTRANSPORT PROTEIN / transporter
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / ABC transporter / ABC transporter
Function and homology information
Biological speciesCaldanaerobius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsAgarwal, V. / Nair, S.K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Biochemical and Structural Insights into Xylan Utilization by the Thermophilic Bacterium Caldanaerobius polysaccharolyticus.
Authors: Han, Y. / Agarwal, V. / Dodd, D. / Kim, J. / Bae, B. / Mackie, R.I. / Nair, S.K. / Cann, I.K.
History
DepositionJul 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter
B: ABC transporter
C: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,7905
Polymers145,9613
Non-polymers8292
Water17,943996
1
A: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8162
Polymers50,4011
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2882
Polymers47,8741
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ABC transporter


Theoretical massNumber of molelcules
Total (without water)47,6861
Polymers47,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.330, 150.862, 150.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC transporter


Mass: 50401.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobius (bacteria) / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / References: UniProt: J9PBT4*PLUS
#2: Protein ABC transporter


Mass: 47873.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobius (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: J9PBT5*PLUS
#3: Protein ABC transporter


Mass: 47686.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobius (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: J9PBT5*PLUS
#4: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a212h-1a_1-5][a212h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 996 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 1500, pH 7.5, vapor diffusion, hanging drop, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D
DetectorDate: Jun 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 126799 / % possible obs: 99.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.094 / Χ2: 2.662 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.867.40.242123111.101198.4
1.86-1.947.80.197125501.2651100
1.94-2.037.80.157125511.4941100
2.03-2.137.90.133126241.743199.9
2.13-2.2780.113125952.0061100
2.27-2.4480.102126182.2651100
2.44-2.698.10.094127012.7211100
2.69-3.088.10.089127413.521100
3.08-3.887.80.083128355.0331100
3.88-507.80.071132735.167199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0056refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.871 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.802 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 6312 5 %RANDOM
Rwork0.2298 ---
obs0.2313 125721 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 80.31 Å2 / Biso mean: 17.5393 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2--0.17 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9150 0 56 996 10202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229411
X-RAY DIFFRACTIONr_angle_refined_deg1.0091.95512748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.53251173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54526.207435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88151578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1921515
X-RAY DIFFRACTIONr_chiral_restr0.0760.21394
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217152
X-RAY DIFFRACTIONr_mcbond_it0.3671.55835
X-RAY DIFFRACTIONr_mcangle_it0.71729354
X-RAY DIFFRACTIONr_scbond_it1.26533576
X-RAY DIFFRACTIONr_scangle_it2.0194.53394
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 460 -
Rwork0.251 8580 -
all-9040 -
obs--100 %

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