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- PDB-4v15: Crystal structure of D-threonine aldolase from Alcaligenes xyloso... -

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Basic information

Entry
Database: PDB / ID: 4v15
TitleCrystal structure of D-threonine aldolase from Alcaligenes xylosoxidans
ComponentsD-THREONINE ALDOLASE
KeywordsLYASE / DEGRADATION / VITAMIN B6- ENZYME FOLD-TYPE III / ALANINE RACEMASE- LIKE DOMAIN
Function / homology
Function and homology information


D-threonine aldolase / D-threonine aldolase activity
Similarity search - Function
D-serine dehydratase-like domain / D-serine dehydratase-like domain / D-serine dehydratase-like domain superfamily / Putative serine dehydratase domain / Putative serine dehydratase domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / PLP-binding barrel ...D-serine dehydratase-like domain / D-serine dehydratase-like domain / D-serine dehydratase-like domain superfamily / Putative serine dehydratase domain / Putative serine dehydratase domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / PYRIDOXAL-5'-PHOSPHATE / D-threonine aldolase
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsUhl, M.K. / Oberdorfer, G. / Steinkellner, G. / Riegler, L. / Schuermann, M. / Gruber, K.
CitationJournal: Plos One / Year: 2015
Title: The Crystal Structure of D-Threonine Aldolase from Alcaligenes Xylosoxidans Provides Insight Into a Metal Ion Assisted Plp-Dependent Mechanism.
Authors: Uhl, M.K. / Oberdorfer, G. / Steinkellner, G. / Riegler-Berket, L. / Mink, D. / Van Assema, F. / Schurmann, M. / Gruber, K.
History
DepositionSep 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _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: D-THREONINE ALDOLASE
B: D-THREONINE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,81710
Polymers79,6722
Non-polymers1,1448
Water17,204955
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-43.6 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.267, 84.278, 72.852
Angle α, β, γ (deg.)90.00, 111.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D-THREONINE ALDOLASE


Mass: 39836.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Strain: IFO 12669
Description: GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES (DSMZ)
Plasmid: PBBVR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: A0A0J9X243*PLUS, D-threonine aldolase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 955 / 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: 2.2 Å3/Da / Density % sol: 45 %
Description: MOLECULAR REPLACEMENT WAS PERFORMED FOLLOWING THE PROTOCOL OF DIMAIO ET AL. EMPLOYING THE PROGRAMS PHASER AND ROSETTA.
Crystal growpH: 8.1
Details: 13% (W/V) PEG-3350, 200 MM SODIUM CHLORIDE, 100 MM TRIS/HCL, PH 8.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9537
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2008 / Details: TOROIDAL FOCUSING
RadiationMonochromator: BARTELS MONOCHROMATOR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→47.65 Å / Num. obs: 111114 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 12.65 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameClassification
AUTOMARdata reduction
SCALEPACKdata scaling
PHASERphasing
Rosettaphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GWQ AND 3LLX

3gwq

3llx


Resolution: 1.5→35.759 Å / SU ML: 0.14 / σ(F): 1.44 / Phase error: 16.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1767 5551 5 %
Rwork0.1484 --
obs0.1499 111114 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.5 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5489 0 66 955 6510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0196010
X-RAY DIFFRACTIONf_angle_d1.3568234
X-RAY DIFFRACTIONf_dihedral_angle_d14.6262236
X-RAY DIFFRACTIONf_chiral_restr0.057937
X-RAY DIFFRACTIONf_plane_restr0.0071103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.23381930.20593570X-RAY DIFFRACTION100
1.5171-1.53490.24031820.20233488X-RAY DIFFRACTION100
1.5349-1.55360.20221880.19253530X-RAY DIFFRACTION100
1.5536-1.57330.22681600.17783465X-RAY DIFFRACTION100
1.5733-1.5940.21411720.17753605X-RAY DIFFRACTION100
1.594-1.61580.20161680.1733505X-RAY DIFFRACTION100
1.6158-1.63890.19721660.16633529X-RAY DIFFRACTION100
1.6389-1.66340.19741810.16543529X-RAY DIFFRACTION100
1.6634-1.68940.1951860.16183571X-RAY DIFFRACTION100
1.6894-1.71710.19941870.16173489X-RAY DIFFRACTION100
1.7171-1.74670.20091850.16283499X-RAY DIFFRACTION100
1.7467-1.77840.19421930.15563545X-RAY DIFFRACTION100
1.7784-1.81260.17181770.15033499X-RAY DIFFRACTION100
1.8126-1.84960.17951770.14973522X-RAY DIFFRACTION100
1.8496-1.88980.17791680.15283568X-RAY DIFFRACTION100
1.8898-1.93380.21371820.17243503X-RAY DIFFRACTION100
1.9338-1.98220.19912010.1643497X-RAY DIFFRACTION100
1.9822-2.03570.18831790.15483528X-RAY DIFFRACTION100
2.0357-2.09560.18412190.15233521X-RAY DIFFRACTION100
2.0956-2.16330.19271800.15313518X-RAY DIFFRACTION100
2.1633-2.24060.18861910.14313545X-RAY DIFFRACTION100
2.2406-2.33030.15661930.15173489X-RAY DIFFRACTION99
2.3303-2.43630.17241930.14153520X-RAY DIFFRACTION100
2.4363-2.56470.16981870.1443539X-RAY DIFFRACTION100
2.5647-2.72540.16942230.15293517X-RAY DIFFRACTION100
2.7254-2.93570.17881930.14363539X-RAY DIFFRACTION100
2.9357-3.2310.1741750.13743543X-RAY DIFFRACTION100
3.231-3.69810.15121850.12733543X-RAY DIFFRACTION100
3.6981-4.65760.14071990.11973480X-RAY DIFFRACTION98
4.6576-35.76930.16581680.14513367X-RAY DIFFRACTION92
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)
10.70840.10560.380.16250.22961.2122-0.00480.0436-0.00050.0018-0.0012-0.0134-0.04220.08060.010.0981-0.00880.0040.05250.00520.106838.79541.457615.3514
20.93870.00840.2830.6031-0.38822.06970.01030.0063-0.0647-0.0564-0.024-0.08460.1440.27510.01080.08950.01230.00160.1056-0.01010.114850.239436.586338.2708
30.59990.11250.35530.31130.00910.6602-0.0061-0.086-0.02980.05330.0234-0.01660.0139-0.038-0.01620.09890.01660.00940.11920.00230.113933.591730.404756.5838
40.9261-0.10070.01010.6198-0.01651.8124-0.01660.0152-0.1147-0.05070.02170.05370.2227-0.06870.00560.0951-0.0107-0.00640.05260.00820.106825.525828.739930.9505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:263)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 264:379)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 8:268)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 269:379)

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