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- PDB-4xg1: Psychromonas ingrahamii diaminopimelate decarboxylase with LLP -

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Basic information

Entry
Database: PDB / ID: 4xg1
TitlePsychromonas ingrahamii diaminopimelate decarboxylase with LLP
ComponentsDiaminopimelate decarboxylase
KeywordsLYASE / lysine biosynthesis / psychrophile / TIM barrel
Function / homology
Function and homology information


diaminopimelate decarboxylase / diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate / pyridoxal phosphate binding
Similarity search - Function
Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain ...Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Chem-LLP / THIOCYANATE ION / PROPANE / Diaminopimelate decarboxylase
Similarity search - Component
Biological speciesPsychromonas ingrahamii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPeverelli, M.G. / Wubben, J.M. / Panjikar, S. / Perugini, M.A.
CitationJournal: To Be Published
Title: Expression to crystallization of diaminopimelate decarboxylase from the psychrophile Psychromonas ingrahamii
Authors: Peverelli, M.G. / Newman, J. / Panjikar, S. / Perugini, M.A.
History
DepositionDec 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diaminopimelate decarboxylase
B: Diaminopimelate decarboxylase
C: Diaminopimelate decarboxylase
D: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,79928
Polymers189,3204
Non-polymers2,47924
Water7,044391
1
A: Diaminopimelate decarboxylase
B: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,09218
Polymers94,6602
Non-polymers1,43216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-29 kcal/mol
Surface area28310 Å2
MethodPISA
2
C: Diaminopimelate decarboxylase
D: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,70710
Polymers94,6602
Non-polymers1,0478
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-38 kcal/mol
Surface area28590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.960, 103.130, 93.590
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 2 - 421 / Label seq-ID: 2 - 421

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Diaminopimelate decarboxylase / / DAPDC


Mass: 47330.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychromonas ingrahamii (bacteria) / Strain: 37 / Gene: lysA, Ping_0041 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1SR00, diaminopimelate decarboxylase

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Non-polymers , 5 types, 415 molecules

#2: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-TME / PROPANE / Propane


Mass: 44.096 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8
#5: Chemical
ChemComp-LLP / (2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid / N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE


Type: L-peptide linking / Mass: 375.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H22N3O7P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.21 Å3/Da / Density % sol: 44.3 % / Description: Triangular prism
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 28%(W/V) PEG 3350, 100mM BIS-TRIS PROPANE (PH 6.0), 200mM POTASSIUM THIOCYANATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K
PH range: 6 / Temp details: Temperature controlled cold room

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: Crystal flash frozen in cold room and stored in puck until data collection
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.5→69.17 Å / Num. obs: 58922 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.072 / Rsym value: 0.077 / Net I/σ(I): 20.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 11.6 / Rsym value: 0.157 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
SHELXAuto-Rickshaw web serverphasing
REFMAC5.8.0073refinement
Cootmodel building
XDSdata reduction
Auto-RickshawWEB SERVERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3N2B

3n2b


Resolution: 2.5→19.85 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.898 / SU B: 10.655 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.806 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24589 1014 1.7 %RANDOM
Rwork0.2113 ---
obs0.2119 57729 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.382 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å20.09 Å2
2---0.03 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12467 0 148 391 13006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01912813
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212468
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9817298
X-RAY DIFFRACTIONr_angle_other_deg1.116328612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59151604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68924.392551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.737152184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9051577
X-RAY DIFFRACTIONr_chiral_restr0.0760.21959
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02114382
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022785
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6883.0426495
X-RAY DIFFRACTIONr_mcbond_other2.6883.0426494
X-RAY DIFFRACTIONr_mcangle_it4.2944.5438065
X-RAY DIFFRACTIONr_mcangle_other4.2944.5428066
X-RAY DIFFRACTIONr_scbond_it2.6363.2926318
X-RAY DIFFRACTIONr_scbond_other2.6353.2926313
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3994.839234
X-RAY DIFFRACTIONr_long_range_B_refined6.88723.68914697
X-RAY DIFFRACTIONr_long_range_B_other6.88623.68914698
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A235010.09
12B235010.09
21A238600.08
22C238600.08
31A235070.08
32D235070.08
41B253970.08
42C253970.08
51B248030.07
52D248030.07
61C250340.07
62D250340.07
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 71 -
Rwork0.303 4219 -
obs--99.93 %

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