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- PDB-7eiw: Human histidine decarboxylase mutant Y334F reacted with histidine -

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Basic information

Entry
Database: PDB / ID: 7eiw
TitleHuman histidine decarboxylase mutant Y334F reacted with histidine
ComponentsHistidine decarboxylase
KeywordsLYASE / Pyridoxal-dependent decarboxylase
Function / homology
Function and homology information


histamine biosynthetic process / histidine decarboxylase / histidine decarboxylase activity / Histidine catabolism / L-histidine metabolic process / L-histidine catabolic process / catecholamine biosynthetic process / amino acid metabolic process / pyridoxal phosphate binding / cytosol / cytoplasm
Similarity search - Function
Aromatic-L-amino-acid decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Histidine decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKomori, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K07272 Japan
CitationJournal: J Biol Macromol / Year: 2021
Title: Structural analysis of the HDC Y334F mutant
Authors: Komori, H. / Nitta, Y.
History
DepositionApr 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine decarboxylase
B: Histidine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1234
Polymers108,6282
Non-polymers4942
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-86 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.902, 57.654, 117.647
Angle α, β, γ (deg.)90.000, 106.297, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histidine decarboxylase / / HDC


Mass: 54314.172 Da / Num. of mol.: 2 / Mutation: C180S, C418S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDC / Production host: Escherichia coli (E. coli) / References: UniProt: P19113, histidine decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.09 Å3/Da / Density % sol: 41.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5), 28% (w/v) PEG 3350, 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 52603 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.431 / Num. unique obs: 5121

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E1O

4e1o


Resolution: 2.1→33.223 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.199 / SU B: 15.764 / SU ML: 0.192 / Average fsc free: 0.8474 / Average fsc work: 0.8684 / Cross valid method: FREE R-VALUE / ESU R: 0.286 / ESU R Free: 0.211
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2521 2679 5.095 %
Rwork0.2119 49904 -
all0.214 --
obs-52583 99.435 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.105 Å2
Baniso -1Baniso -2Baniso -3
1-0.775 Å2-0 Å22.994 Å2
2---0.971 Å2-0 Å2
3----1.328 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7431 0 30 151 7612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137697
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177229
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.63810451
X-RAY DIFFRACTIONr_angle_other_deg1.1521.57416664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9215942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9321.535404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.301151302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0551555
X-RAY DIFFRACTIONr_chiral_restr0.0570.2983
X-RAY DIFFRACTIONr_chiral_restr_other0.0390.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021804
X-RAY DIFFRACTIONr_nbd_refined0.190.21609
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.26854
X-RAY DIFFRACTIONr_nbtor_refined0.1590.23684
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.23589
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0240.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.213
X-RAY DIFFRACTIONr_nbd_other0.1830.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.26
X-RAY DIFFRACTIONr_mcbond_it1.264.0323744
X-RAY DIFFRACTIONr_mcbond_other1.2584.0323743
X-RAY DIFFRACTIONr_mcangle_it2.0436.044676
X-RAY DIFFRACTIONr_mcangle_other2.0436.044677
X-RAY DIFFRACTIONr_scbond_it1.1674.2133953
X-RAY DIFFRACTIONr_scbond_other1.1614.2143950
X-RAY DIFFRACTIONr_scangle_it1.9546.2655769
X-RAY DIFFRACTIONr_scangle_other1.9546.2665770
X-RAY DIFFRACTIONr_lrange_it3.53346.9368620
X-RAY DIFFRACTIONr_lrange_other3.52746.9278611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.3511830.33635000.33738820.5520.57794.87380.3
2.154-2.2130.3362090.32335270.32437760.6430.67698.94070.29
2.213-2.2770.3311680.27534820.27836570.7670.80799.80860.242
2.277-2.3470.2781950.25633260.25835220.8430.8599.97160.223
2.347-2.4230.3061700.24133150.24434850.8620.8731000.208
2.423-2.5080.2891590.22732080.2333670.8790.8991000.197
2.508-2.6020.281590.22130600.22432190.8880.9131000.19
2.602-2.7070.261630.22629180.22830820.8830.9199.96760.197
2.707-2.8270.3051440.2328760.23430200.8830.9111000.203
2.827-2.9640.2671500.22126740.22428240.8910.9191000.197
2.964-3.1230.3061330.2226320.22427650.8820.9121000.202
3.123-3.310.241280.20724370.20925650.9170.9311000.193
3.31-3.5370.2291150.20623140.20724310.9330.9499.91770.198
3.537-3.8160.2411370.19621430.19922820.9280.9499.91240.191
3.816-4.1750.2081080.18919710.1920790.9440.9471000.191
4.175-4.6590.1981090.16818030.1719140.9550.96199.89550.176
4.659-5.3620.222800.16816230.1717030.9540.9661000.177
5.362-6.5240.253770.19213580.19514350.9160.9551000.203
6.524-9.0540.21600.17710830.17811440.9450.96199.91260.19
9.054-33.2230.239320.2116500.2137020.9580.96297.1510.231
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)
10.3249-0.218-0.26120.23410.45061.1609-0.06120.04910.01840.135-0.07190.0450.3059-0.16250.1330.1256-0.05340.07090.026-0.02470.051-22.8796-7.3843-22.0227
20.1174-0.1535-0.20280.43890.22440.3579-0.0351-0.02430.04580.04610.1146-0.04720.06050.0285-0.07950.0157-0.0009-0.00670.0652-0.03140.05710.2982-13.1638-35.4843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 477
2X-RAY DIFFRACTION2ALLB1 - 476

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