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- PDB-4r1p: Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arab... -

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Basic information

Entry
Database: PDB / ID: 4r1p
TitleCrystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase with Mn2+
ComponentsL-arabinose isomerase
KeywordsISOMERASE / Hexamer / Themophile / Thermostable / AI fold
Function / homology
Function and homology information


L-arabinose isomerase / L-arabinose isomerase activity / L-arabinose catabolic process to D-xylulose 5-phosphate / manganese ion binding / cytosol
Similarity search - Function
Rossmann fold - #10940 / : / : / L-arabinose isomerase central domain / L-arabinose isomerase / L-arabinose isomerase, C-terminal / L-arabinose isomerase, N-terminal domain superfamily / L-arabinose isomerase N-terminal domain / L-arabinose isomerase C-terminal domain / L-fucose/L-arabinose isomerase, C-terminal ...Rossmann fold - #10940 / : / : / L-arabinose isomerase central domain / L-arabinose isomerase / L-arabinose isomerase, C-terminal / L-arabinose isomerase, N-terminal domain superfamily / L-arabinose isomerase N-terminal domain / L-arabinose isomerase C-terminal domain / L-fucose/L-arabinose isomerase, C-terminal / L-fucose isomerase, N-terminal/central domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / L-arabinose isomerase
Similarity search - Component
Biological speciesGeobacillus kaustophilus HTA426 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 Å
AuthorsChoi, J.M. / Lee, Y.J. / Lee, D.W. / Lee, S.H.
CitationJournal: To be Published
Title: Crystal Structure of Thermophilic L-Arabinose with Mn2+ from Geobacillus kaustophilus
Authors: Choi, J.M. / Lee, Y.J. / Lee, D.W. / Lee, S.H.
History
DepositionAug 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Structure summary
Revision 1.2Nov 8, 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
D: L-arabinose isomerase
E: L-arabinose isomerase
F: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,15912
Polymers337,8296
Non-polymers3306
Water21,0961171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40120 Å2
ΔGint-240 kcal/mol
Surface area89520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.659, 153.120, 91.239
Angle α, β, γ (deg.)90.00, 103.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
L-arabinose isomerase


Mass: 56304.891 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus HTA426 (bacteria)
Gene: araA, GK1904 / Plasmid: pET28a(+)-GKAI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5KYP7, L-arabinose isomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1171 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS RESIDUE IS BASED ON YP_147757 OF GENBANK.

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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: 45.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M imidazole hydrochloric acid, 1M sodium citrate tribasic, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2013
RadiationMonochromator: DCM Si(111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.297→50 Å / Num. all: 131054 / Num. obs: 131054 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 28.33 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 18.333
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 2.818 / Num. unique all: 6492 / Rsym value: 0.833 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AJT

2ajt


Resolution: 2.297→43.694 Å / FOM work R set: 0.8507 / SU ML: 0.25 / σ(F): 1.35 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 6587 5.03 %Random
Rwork0.1555 ---
obs0.1584 131032 98.88 %-
all-131032 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.06 Å2 / Biso mean: 13.18 Å2 / Biso min: 0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.297→43.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23591 0 6 1171 24768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824185
X-RAY DIFFRACTIONf_angle_d1.09432754
X-RAY DIFFRACTIONf_chiral_restr0.0733466
X-RAY DIFFRACTIONf_plane_restr0.0054293
X-RAY DIFFRACTIONf_dihedral_angle_d15.2048822
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2971-2.32320.31061840.23393384356882
2.3232-2.35050.28652140.21374169438399
2.3505-2.37920.29622140.21164165437999
2.3792-2.40930.30012130.21584121433499
2.4093-2.4410.28812120.21764118433099
2.441-2.47440.29432060.2074177438399
2.4744-2.50980.27652050.20474179438499
2.5098-2.54730.26392250.18754129435499
2.5473-2.5870.262090.18934125433499
2.587-2.62950.26182170.18234119433699
2.6295-2.67480.2662340.18124154438899
2.6748-2.72340.27222290.18254134436399
2.7234-2.77580.25162270.1724173440099
2.7758-2.83240.24122340.1684140437499
2.8324-2.8940.25062120.16284142435499
2.894-2.96130.23232210.168941894410100
2.9613-3.03540.25042220.157541414363100
3.0354-3.11740.20242290.149742074436100
3.1174-3.20910.21972040.150541654369100
3.2091-3.31270.20822020.152542494451100
3.3127-3.4310.2122240.141341924416100
3.431-3.56830.19172210.139541964417100
3.5683-3.73070.19692160.135742104426100
3.7307-3.92720.1752250.129741864411100
3.9272-4.17310.17542230.126741914414100
4.1731-4.4950.16972470.124141934440100
4.495-4.94680.16052500.122241714421100
4.9468-5.66130.18562290.138342254454100
5.6613-7.12760.17392160.161142484464100
7.1276-43.70160.17072230.15084253447699

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