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- PDB-7ch3: Crystal structure of Arabinose isomerase from hyper thermophilic ... -

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Basic information

Entry
Database: PDB / ID: 7ch3
TitleCrystal structure of Arabinose isomerase from hyper thermophilic bacterium Thermotoga maritima (TMAI) triple mutant (K264A, E265A, K266A)
ComponentsL-arabinose isomerase
KeywordsISOMERASE / Arabinose isomerase from hyperthermophile
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 / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.61 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 Arabinose isomerase from hyper thermophilic bacterium Thermotoga maritima (TMAI) triple mutant (K264A, E265A, K266A)
Authors: Cao, T.P. / Dhanasingh, I. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H.
History
DepositionJul 4, 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: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
D: L-arabinose isomerase
E: L-arabinose isomerase
F: L-arabinose isomerase
G: L-arabinose isomerase
H: L-arabinose isomerase
I: L-arabinose isomerase
J: L-arabinose isomerase
K: L-arabinose isomerase
L: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)679,73330
Polymers678,74412
Non-polymers98918
Water34219
1
A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
D: L-arabinose isomerase
F: L-arabinose isomerase
H: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,86615
Polymers339,3726
Non-polymers4949
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43730 Å2
ΔGint-254 kcal/mol
Surface area92760 Å2
MethodPISA
2
E: L-arabinose isomerase
G: L-arabinose isomerase
I: L-arabinose isomerase
J: L-arabinose isomerase
K: L-arabinose isomerase
L: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,86615
Polymers339,3726
Non-polymers4949
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43910 Å2
ΔGint-246 kcal/mol
Surface area94020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.424, 113.913, 160.833
Angle α, β, γ (deg.)81.080, 81.150, 88.890
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 1 through 218 or resid 245 through 495))
31(chain C and (resid 1 through 218 or resid 245 through 495))
41(chain D and (resid 1 through 218 or resid 245 through 495))
51(chain E and (resid 1 through 218 or resid 245 through 495))
61(chain F and (resid 1 through 218 or resid 245 through 495))
71(chain G and (resid 1 through 218 or resid 245 through 495))
81(chain H and (resid 1 through 218 or resid 245 through 495))
91(chain I and (resid 1 through 218 or resid 245 through 495))
101(chain J and (resid 1 through 218 or resid 245 through 495))
111(chain K and (resid 1 through 218 or resid 245 through 495))
121(chain L and (resid 1 through 218 or resid 245 through 495))

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
11METMETLYSLYSchain AAA1 - 4951 - 495
21METMETVALVAL(chain B and (resid 1 through 218 or resid 245 through 495))BB1 - 2181 - 218
22SERSERLYSLYS(chain B and (resid 1 through 218 or resid 245 through 495))BB245 - 495245 - 495
31METMETVALVAL(chain C and (resid 1 through 218 or resid 245 through 495))CC1 - 2181 - 218
32SERSERLYSLYS(chain C and (resid 1 through 218 or resid 245 through 495))CC245 - 495245 - 495
41METMETVALVAL(chain D and (resid 1 through 218 or resid 245 through 495))DD1 - 2181 - 218
42SERSERLYSLYS(chain D and (resid 1 through 218 or resid 245 through 495))DD245 - 495245 - 495
51METMETVALVAL(chain E and (resid 1 through 218 or resid 245 through 495))EE1 - 2181 - 218
52SERSERLYSLYS(chain E and (resid 1 through 218 or resid 245 through 495))EE245 - 495245 - 495
61METMETVALVAL(chain F and (resid 1 through 218 or resid 245 through 495))FF1 - 2181 - 218
62SERSERLYSLYS(chain F and (resid 1 through 218 or resid 245 through 495))FF245 - 495245 - 495
71METMETVALVAL(chain G and (resid 1 through 218 or resid 245 through 495))GG1 - 2181 - 218
72SERSERLYSLYS(chain G and (resid 1 through 218 or resid 245 through 495))GG245 - 495245 - 495
81METMETVALVAL(chain H and (resid 1 through 218 or resid 245 through 495))HH1 - 2181 - 218
82SERSERLYSLYS(chain H and (resid 1 through 218 or resid 245 through 495))HH245 - 495245 - 495
91METMETVALVAL(chain I and (resid 1 through 218 or resid 245 through 495))II1 - 2181 - 218
92SERSERLYSLYS(chain I and (resid 1 through 218 or resid 245 through 495))II245 - 495245 - 495
101METMETVALVAL(chain J and (resid 1 through 218 or resid 245 through 495))JJ1 - 2181 - 218
102SERSERLYSLYS(chain J and (resid 1 through 218 or resid 245 through 495))JJ245 - 495245 - 495
111METMETVALVAL(chain K and (resid 1 through 218 or resid 245 through 495))KK1 - 2181 - 218
112SERSERLYSLYS(chain K and (resid 1 through 218 or resid 245 through 495))KK245 - 495245 - 495
121METMETVALVAL(chain L and (resid 1 through 218 or resid 245 through 495))LL1 - 2181 - 218
122SERSERLYSLYS(chain L and (resid 1 through 218 or resid 245 through 495))LL245 - 495245 - 495

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Components

#1: Protein
L-arabinose isomerase


Mass: 56561.984 Da / Num. of mol.: 12 / Mutation: K264A, E265A, K266A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: araA, TM_0276 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WYB3, L-arabinose isomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / Details: 100mM Tris pH 8.5, 2% Tacismate pH 8, 15% PEG 3350

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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: 3.6→50 Å / Num. obs: 68198 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.053 / Rrim(I) all: 0.102 / Χ2: 0.707 / Net I/σ(I): 9 / Num. measured all: 252359
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.6-3.663.60.48633690.6320.2970.571197.3
3.66-3.733.70.41133740.6860.2540.4851.01597.8
3.73-3.83.60.34734280.8540.2110.4070.79497.9
3.8-3.883.70.36733590.8880.2230.4310.81998.1
3.88-3.963.70.27434520.920.1660.3210.76798.2
3.96-4.053.70.22633650.9320.1380.2650.76498.6
4.05-4.163.70.19933940.9470.1210.2330.7998.5
4.16-4.273.70.16834000.9290.1020.1980.84999
4.27-4.393.70.13834940.890.0850.1631.03999.2
4.39-4.543.80.09934250.970.060.1160.73399.3
4.54-4.73.80.07534020.980.0450.0870.76899.2
4.7-4.893.80.06234690.9790.0360.0720.62999.4
4.89-5.113.80.05834300.9810.0340.0670.58499.5
5.11-5.383.80.05634330.980.0330.0650.5799.5
5.38-5.713.80.05734480.9730.0340.0670.56899.6
5.71-6.153.80.04834500.9760.0280.0560.50299.6
6.15-6.773.80.03834580.9830.0220.0440.48199.7
6.77-7.753.70.02634260.9890.0160.0310.45799.7
7.75-9.753.60.02134430.9880.0120.0240.49199.1
9.75-503.20.02231790.9890.0140.0260.54392.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HXG

2hxg


Resolution: 3.61→33.11 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2799 3336 4.98 %
Rwork0.2316 63677 -
obs0.2341 67013 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.2 Å2 / Biso mean: 73.6774 Å2 / Biso min: 15.86 Å2
Refinement stepCycle: final / Resolution: 3.61→33.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47398 0 18 19 47435
Biso mean--90.91 35.7 -
Num. residues----5914
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A17076X-RAY DIFFRACTION7.063TORSIONAL
12B17076X-RAY DIFFRACTION7.063TORSIONAL
13C17076X-RAY DIFFRACTION7.063TORSIONAL
14D17076X-RAY DIFFRACTION7.063TORSIONAL
15E17076X-RAY DIFFRACTION7.063TORSIONAL
16F17076X-RAY DIFFRACTION7.063TORSIONAL
17G17076X-RAY DIFFRACTION7.063TORSIONAL
18H17076X-RAY DIFFRACTION7.063TORSIONAL
19I17076X-RAY DIFFRACTION7.063TORSIONAL
110J17076X-RAY DIFFRACTION7.063TORSIONAL
111K17076X-RAY DIFFRACTION7.063TORSIONAL
112L17076X-RAY DIFFRACTION7.063TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.61-3.660.3004980.28671835193365
3.66-3.710.34251280.29062336246485
3.71-3.770.33881180.27762488260690
3.77-3.830.30291510.28162627277895
3.83-3.90.31951420.27732633277596
3.9-3.970.29891430.27692740288397
3.97-4.050.30051270.26012671279898
4.05-4.130.32521280.26342714284298
4.13-4.220.31351440.27032725286998
4.22-4.320.33981470.27242710285799
4.32-4.420.29171460.24992709285598
4.42-4.540.26831310.22622767289899
4.54-4.680.27451560.21282712286899
4.68-4.830.28341480.2132743289199
4.83-50.26781330.21422742287599
5-5.20.23791560.207327602916100
5.2-5.430.32291280.22222760288899
5.43-5.720.26231400.230127402880100
5.72-6.070.27481560.226527262882100
6.07-6.540.30591380.240127462884100
6.54-7.190.25951690.215627492918100
7.19-8.220.20571380.177927402878100
8.22-10.30.21291550.16592724287999
10.3-33.110.28361160.2122580269693
Refinement TLS params.Method: refined / Origin x: -18.4847 Å / Origin y: -4.1574 Å / Origin z: -16.3098 Å
111213212223313233
T0.1153 Å20.0087 Å20.1375 Å2-0.1342 Å2-0.0956 Å2--0.2946 Å2
L0.5814 °2-0.1722 °20.4299 °2-0.3642 °2-0.2957 °2--1.007 °2
S-0.0247 Å °0.0513 Å °0.043 Å °-0.0501 Å °-0.0062 Å °-0.0464 Å °0.1275 Å °-0.086 Å °0.0153 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 495
2X-RAY DIFFRACTION1allB1 - 495
3X-RAY DIFFRACTION1allC1 - 495
4X-RAY DIFFRACTION1allD1 - 495
5X-RAY DIFFRACTION1allE1 - 495
6X-RAY DIFFRACTION1allF1 - 495
7X-RAY DIFFRACTION1allG1 - 495
8X-RAY DIFFRACTION1allH1 - 495
9X-RAY DIFFRACTION1allI1 - 495
10X-RAY DIFFRACTION1allJ1 - 495
11X-RAY DIFFRACTION1allK1 - 495
12X-RAY DIFFRACTION1allL1 - 495
13X-RAY DIFFRACTION1allM1 - 18
14X-RAY DIFFRACTION1allN1 - 19

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