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- PDB-4k8g: Crystal structure of D-Mannonate dehydratase from Novosphingobium... -

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Basic information

Entry
Database: PDB / ID: 4k8g
TitleCrystal structure of D-Mannonate dehydratase from Novosphingobium aromaticivorans mutant (V161A, R163A, K165G, L166A, Y167G, Y168A, E169G)
ComponentsMandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
KeywordsMETAL BINDING PROTEIN / TIM barrel
Function / homology
Function and homology information


mannonate dehydratase / mannonate dehydratase activity / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
D-mannonate dehydratase / D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like ...D-mannonate dehydratase / D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D-mannonate dehydratase
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsLukk, T. / Wichelecki, D. / Gerlt, J.A. / Nair, S.K.
CitationJournal: To be Published
Title: Crystal structure of D-Mannonate dehydratase from Novosphingobium aromaticivorans mutant (V161A, R163A, K165G, L166A, Y167G, Y168A, E169G)
Authors: Wichelecki, D. / Lukk, T. / Nair, S.K. / Gerlt, J.A.
History
DepositionApr 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.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_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_ref_seq_dif.details / _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: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0873
Polymers46,9701
Non-polymers1162
Water9,620534
1
A: Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)376,69224
Polymers375,7618
Non-polymers93116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
crystal symmetry operation5_757-x+2,y,-z+21
crystal symmetry operation6_577x,-y+2,-z+21
crystal symmetry operation7_557y,x,-z+21
crystal symmetry operation8_777-y+2,-x+2,-z+21
Buried area50940 Å2
ΔGint-197 kcal/mol
Surface area80280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.770, 125.770, 119.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-610-

HOH

21A-682-

HOH

31A-730-

HOH

41A-816-

HOH

51A-888-

HOH

61A-1044-

HOH

71A-1086-

HOH

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Components

#1: Protein Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein


Mass: 46970.109 Da / Num. of mol.: 1 / Mutation: V161A, R163A, K165G, L166A, Y167G, Y168A, E169G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_3675 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4XF23
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Mother liqueur contained 28% PEG 400, 100 mM HEPES, NaOH, 200 mM Calcium chloride. Protein solution was at 20 mg/mL, 100 mM NaCl, 50 mM Tris, pH 7.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Jan 1, 2003
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.25→29.9 Å / Num. all: 131226 / Num. obs: 131204 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.263 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 18.84
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.25-1.280.7663.8415307896121100
1.28-1.320.6384.6214973493771100
1.32-1.360.5425.4914634491261100
1.36-1.40.456.5814210888421100
1.4-1.440.3678.0113874486091100
1.44-1.490.3029.6913417183051100
1.49-1.550.23912.1612998980441100
1.55-1.610.19514.6612476977351100
1.61-1.690.16417.1911975074321100
1.69-1.770.1419.9911446371101100
1.77-1.860.11623.4110819067591100
1.86-1.980.09927.1910277364511100
1.98-2.110.08331.439487860241100
2.11-2.280.07434.968883356591100
2.28-2.50.06737.618136451901100
2.5-2.80.06139.997374647271100
2.8-3.230.05742.956502441991100
3.23-3.950.05145.195480635751100
3.95-5.590.04746.924298628041100
5.59-29.90.04445.48235781624199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→29.9 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9319 / SU ML: 0.08 / σ(F): 2 / Phase error: 12.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1482 6560 5 %random
Rwork0.141 ---
obs0.1413 131191 99.98 %-
all-131204 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.81 Å2 / Biso mean: 12.2156 Å2 / Biso min: 4.97 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 7 534 3613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063281
X-RAY DIFFRACTIONf_angle_d1.1384479
X-RAY DIFFRACTIONf_chiral_restr0.076477
X-RAY DIFFRACTIONf_plane_restr0.006585
X-RAY DIFFRACTIONf_dihedral_angle_d13.551192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.25-1.26420.19652160.186141174333
1.2642-1.27910.17962160.182140984314
1.2791-1.29470.20412170.177141314348
1.2947-1.3110.17132160.168140954311
1.311-1.32830.16782170.162141214338
1.3283-1.34650.17242170.160341304347
1.3465-1.36570.15982160.155741044320
1.3657-1.38610.16392160.156641044320
1.3861-1.40780.15822180.148841244342
1.4078-1.43090.16142170.147541294346
1.4309-1.45550.14522160.14140994315
1.4555-1.4820.15582180.137141454363
1.482-1.51050.13412170.133641274344
1.5105-1.54130.14842170.130841204337
1.5413-1.57480.14792180.131841494367
1.5748-1.61150.14672170.12941104327
1.6115-1.65180.14492170.128941364353
1.6518-1.69640.14322190.127541554374
1.6964-1.74630.13912180.13241444362
1.7463-1.80270.14752180.132641334351
1.8027-1.86710.14312180.13341594377
1.8671-1.94190.15862200.134741674387
1.9419-2.03020.15462190.133941704389
2.0302-2.13720.13892200.136341704390
2.1372-2.27110.15122180.131441494367
2.2711-2.44640.15082220.139742144436
2.4464-2.69240.14362210.142441914412
2.6924-3.08170.14262220.144842314453
3.0817-3.88130.13892250.137242644489
3.8813-29.94360.13582340.145644454679
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)
10.35420.107-0.12950.19220.12770.2112-0.02490.05190.1055-0.01350.0184-0.0118-0.16420.01460.05020.1283-0.0235-0.01390.09440.00310.1114147.9421169.5587122.4662
20.175-0.009-0.03230.15290.02550.2955-0.00190.0070.0378-0.0125-0.0026-0.0103-0.05960.01280.00390.0938-0.0148-0.01530.06310.00240.0847140.3135161.8566121.8701
30.67530.2486-0.52330.1554-0.03460.87480.0189-0.0833-0.00550.0284-0.0258-0.0743-0.04870.133-00.1253-0.011-0.02990.1227-0.01740.115143.1527150.0026151.4214
40.3276-0.0221-0.00150.3036-0.04680.3354-0.0058-0.04330.00680.043-0.0089-0.0161-0.00280.02330.01680.0692-0.0051-0.00910.0627-0.00010.0634137.0833139.2639140.7904
50.42820.334-0.05240.79880.01680.19580.0057-0.04820.06590.0305-0.01720.0181-0.06970.01950.0110.0851-0.0032-0.01630.0683-0.0070.0693134.1526159.0959132.6575
60.2108-0.1398-0.00712.0848-0.24640.2368-0.0194-0.05180.03760.07120.0225-0.0667-0.05990.05220.0060.1067-0.0262-0.01620.1096-0.00290.0884155.9945152.4615135.8206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 24 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 127 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 177 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 178 through 275 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 276 through 375 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 376 through 402 )A0

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