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- PDB-7chl: Crystal structure of hybrid Arabinose isomerase AI-10 -

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Basic information

Entry
Database: PDB / ID: 7chl
TitleCrystal structure of hybrid Arabinose isomerase AI-10
ComponentsHybrid Arabinose isomerase
KeywordsISOMERASE / hybrid Arabinose isomerase
Function / homology
Function and homology information


L-arabinose isomerase / L-arabinose isomerase activity / L-arabinose catabolic process to D-xylulose 5-phosphate / arabinose catabolic process / 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 / L-arabinose isomerase / L-arabinose isomerase
Similarity search - Component
Biological speciesAlicyclobacillus sp. TP-7 (bacteria)
Geobacillus kaustophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsCao, T.P. / Dhanasingh, I. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H.
CitationJournal: To Be Published
Title: Crystal structure of hybrid Arabinose isomerase AI-10
Authors: Cao, T.P. / Dhanasingh, I. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H.
History
DepositionJul 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hybrid Arabinose isomerase
B: Hybrid Arabinose isomerase
C: Hybrid Arabinose isomerase
D: Hybrid Arabinose isomerase
E: Hybrid Arabinose isomerase
F: Hybrid Arabinose isomerase
G: Hybrid Arabinose isomerase
H: Hybrid Arabinose isomerase
I: Hybrid Arabinose isomerase
J: Hybrid Arabinose isomerase
K: Hybrid Arabinose isomerase
L: Hybrid Arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)671,95836
Polymers671,02212
Non-polymers93524
Water21612
1
A: Hybrid Arabinose isomerase
B: Hybrid Arabinose isomerase
C: Hybrid Arabinose isomerase
D: Hybrid Arabinose isomerase
E: Hybrid Arabinose isomerase
F: Hybrid Arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,97918
Polymers335,5116
Non-polymers46812
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42420 Å2
ΔGint-272 kcal/mol
Surface area92650 Å2
MethodPISA
2
G: Hybrid Arabinose isomerase
H: Hybrid Arabinose isomerase
I: Hybrid Arabinose isomerase
J: Hybrid Arabinose isomerase
K: Hybrid Arabinose isomerase
L: Hybrid Arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,97918
Polymers335,5116
Non-polymers46812
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42500 Å2
ΔGint-280 kcal/mol
Surface area92340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.086, 164.297, 151.973
Angle α, β, γ (deg.)90.000, 119.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 59 or resid 61 through 497))
21(chain B and (resid 2 through 59 or resid 61 through 497))
31(chain C and (resid 2 through 59 or resid 61 through 497))
41(chain D and (resid 2 through 59 or resid 61 through 497))
51(chain E and (resid 2 through 59 or resid 61 through 497))
61(chain F and (resid 2 through 59 or resid 61 through 497))
71(chain G and (resid 2 through 59 or resid 61 through 497))
81(chain H and (resid 2 through 59 or resid 61 through 497))
91(chain I and (resid 2 through 59 or resid 61 through 497))
101(chain J and (resid 2 through 59 or resid 61 through 497))
111(chain K and (resid 2 through 59 or resid 61 through 497))
121(chain L and (resid 2 through 59 or resid 61 through 497))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSILEILE(chain A and (resid 2 through 59 or resid 61 through 497))AA2 - 592 - 59
12ARGARGGLYGLY(chain A and (resid 2 through 59 or resid 61 through 497))AA61 - 49761 - 497
21LYSLYSILEILE(chain B and (resid 2 through 59 or resid 61 through 497))BB2 - 592 - 59
22ARGARGGLYGLY(chain B and (resid 2 through 59 or resid 61 through 497))BB61 - 49761 - 497
31LYSLYSILEILE(chain C and (resid 2 through 59 or resid 61 through 497))CC2 - 592 - 59
32ARGARGGLYGLY(chain C and (resid 2 through 59 or resid 61 through 497))CC61 - 49761 - 497
41LYSLYSILEILE(chain D and (resid 2 through 59 or resid 61 through 497))DD2 - 592 - 59
42ARGARGGLYGLY(chain D and (resid 2 through 59 or resid 61 through 497))DD61 - 49761 - 497
51LYSLYSILEILE(chain E and (resid 2 through 59 or resid 61 through 497))EE2 - 592 - 59
52ARGARGGLYGLY(chain E and (resid 2 through 59 or resid 61 through 497))EE61 - 49761 - 497
61LYSLYSILEILE(chain F and (resid 2 through 59 or resid 61 through 497))FF2 - 592 - 59
62ARGARGGLYGLY(chain F and (resid 2 through 59 or resid 61 through 497))FF61 - 49761 - 497
71LYSLYSILEILE(chain G and (resid 2 through 59 or resid 61 through 497))GG2 - 592 - 59
72ARGARGGLYGLY(chain G and (resid 2 through 59 or resid 61 through 497))GG61 - 49761 - 497
81LYSLYSILEILE(chain H and (resid 2 through 59 or resid 61 through 497))HH2 - 592 - 59
82ARGARGGLYGLY(chain H and (resid 2 through 59 or resid 61 through 497))HH61 - 49761 - 497
91LYSLYSILEILE(chain I and (resid 2 through 59 or resid 61 through 497))II2 - 592 - 59
92ARGARGGLYGLY(chain I and (resid 2 through 59 or resid 61 through 497))II61 - 49761 - 497
101LYSLYSILEILE(chain J and (resid 2 through 59 or resid 61 through 497))JJ2 - 592 - 59
102ARGARGGLYGLY(chain J and (resid 2 through 59 or resid 61 through 497))JJ61 - 49761 - 497
111LYSLYSILEILE(chain K and (resid 2 through 59 or resid 61 through 497))KK2 - 592 - 59
112ARGARGGLYGLY(chain K and (resid 2 through 59 or resid 61 through 497))KK61 - 49761 - 497
121LYSLYSILEILE(chain L and (resid 2 through 59 or resid 61 through 497))LL2 - 592 - 59
122ARGARGGLYGLY(chain L and (resid 2 through 59 or resid 61 through 497))LL61 - 49761 - 497

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Components

#1: Protein
Hybrid Arabinose isomerase / L-arabinose isomerase


Mass: 55918.539 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus sp. TP-7 (bacteria), (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria), (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: araA, araA, GK1904, araA, b0062, JW0061 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: K0IGW6, UniProt: Q5KYP7, UniProt: P08202, L-arabinose isomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 3350, 0.1M Tris pH 8.5, 2% Tacismate pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 84659 / % possible obs: 95.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.05 / Rrim(I) all: 0.129 / Χ2: 0.828 / Net I/σ(I): 8.7 / Num. measured all: 544079
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.466.90.42540860.9280.1730.460.85192
3.46-3.526.90.37440850.9510.1530.4050.87593.1
3.52-3.596.90.35340620.9490.1440.3820.85692.7
3.59-3.666.70.28341220.9530.1170.3070.9393
3.66-3.746.70.24140960.960.10.2610.98793.1
3.74-3.836.70.21241060.9720.0880.2310.93193.2
3.83-3.926.60.17741770.9790.0740.1920.87693.7
3.92-4.036.60.15340510.9820.0640.1660.87393.8
4.03-4.156.50.13441850.9840.0560.1460.88994.2
4.15-4.286.40.11341980.9870.0480.1230.87295.1
4.28-4.446.10.0942160.990.0390.0980.93895.5
4.44-4.616.30.07642680.9920.0330.0830.88796
4.61-4.826.20.06543050.9940.0290.0710.80897.7
4.82-5.086.20.06343990.9940.0280.0690.75998.4
5.08-5.46.30.0643490.9930.0260.0660.71998.8
5.4-5.816.40.06243920.9940.0270.0670.70499.4
5.81-6.46.40.05944270.9940.0260.0650.66699.6
6.4-7.326.40.04844340.9940.0210.0530.66499.5
7.32-9.216.10.0444200.9970.0170.0440.70899.5
9.21-505.50.03842810.9960.0180.0420.76693.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R1O

4r1o


Resolution: 3.4→30.54 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2642 4249 5.03 %
Rwork0.208 80202 -
obs0.2108 84451 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.4 Å2 / Biso mean: 51.1456 Å2 / Biso min: 19.88 Å2
Refinement stepCycle: final / Resolution: 3.4→30.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47131 0 24 12 47167
Biso mean--42.7 30.33 -
Num. residues----5969
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A18096X-RAY DIFFRACTION14.559TORSIONAL
12B18096X-RAY DIFFRACTION14.559TORSIONAL
13C18096X-RAY DIFFRACTION14.559TORSIONAL
14D18096X-RAY DIFFRACTION14.559TORSIONAL
15E18096X-RAY DIFFRACTION14.559TORSIONAL
16F18096X-RAY DIFFRACTION14.559TORSIONAL
17G18096X-RAY DIFFRACTION14.559TORSIONAL
18H18096X-RAY DIFFRACTION14.559TORSIONAL
19I18096X-RAY DIFFRACTION14.559TORSIONAL
110J18096X-RAY DIFFRACTION14.559TORSIONAL
111K18096X-RAY DIFFRACTION14.559TORSIONAL
112L18096X-RAY DIFFRACTION14.559TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.440.32971160.26022473258987
3.44-3.480.30861710.25242528269993
3.48-3.530.33851170.24992565268292
3.53-3.570.32531260.26712585271192
3.57-3.620.27951420.25982613275592
3.62-3.670.38171310.25822550268193
3.67-3.720.37911160.24892624274092
3.72-3.770.27851460.23172547269393
3.77-3.830.27481500.2392610276093
3.83-3.90.25391830.2182564274794
3.9-3.960.30051140.2242593270794
3.96-4.040.37821330.22432652278593
4.04-4.110.26681390.2322670280993
4.11-4.20.2761350.21092568270394
4.2-4.290.23681260.21462665279195
4.29-4.390.23651310.2132729286095
4.39-4.50.23811260.19282694282096
4.5-4.620.29491420.19352715285796
4.62-4.750.25031270.18742718284597
4.75-4.910.26541350.19432750288598
4.91-5.080.24171400.19332800294099
5.08-5.280.23521670.1862672283999
5.28-5.520.23491720.20272772294499
5.52-5.810.2721560.20062764292099
5.81-6.170.25551740.213428072981100
6.17-6.640.26211470.20928182965100
6.64-7.30.23571300.19322801293199
7.3-8.340.20481770.171627972974100
8.34-10.440.20321480.15382806295499
10.45-30.540.2551320.18282752288494
Refinement TLS params.Method: refined / Origin x: 0.1553 Å / Origin y: -40.1143 Å / Origin z: 43.9344 Å
111213212223313233
T0.1831 Å2-0.0104 Å2-0.0117 Å2-0.2593 Å20.019 Å2--0.1896 Å2
L0.084 °2-0.0474 °2-0.0318 °2-0.2493 °20.0864 °2--0.1292 °2
S0.002 Å °0.0115 Å °0.0099 Å °0.0084 Å °0.0091 Å °-0.0232 Å °0.0113 Å °-0.0174 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 498
2X-RAY DIFFRACTION1allB1 - 497
3X-RAY DIFFRACTION1allC1 - 498
4X-RAY DIFFRACTION1allD1 - 498
5X-RAY DIFFRACTION1allE1 - 497
6X-RAY DIFFRACTION1allF2 - 497
7X-RAY DIFFRACTION1allG1 - 498
8X-RAY DIFFRACTION1allH1 - 497
9X-RAY DIFFRACTION1allI1 - 498
10X-RAY DIFFRACTION1allJ1 - 498
11X-RAY DIFFRACTION1allK1 - 498
12X-RAY DIFFRACTION1allL2 - 497
13X-RAY DIFFRACTION1allM1 - 12
14X-RAY DIFFRACTION1allN1 - 12
15X-RAY DIFFRACTION1allO1 - 12

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