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- PDB-1ibt: STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE AT-170 C -

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Basic information

Entry
Database: PDB / ID: 1ibt
TitleSTRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE AT-170 C
Components
  • HISTIDINE DECARBOXYLASE ALPHA CHAIN
  • HISTIDINE DECARBOXYLASE BETA CHAIN
KeywordsLYASE / HELIX DISORDER / LESS ACTIVE FORM / SITE-DIRECTED MUTANT / PYRUVOYL / CARBOXY-LYASE
Function / homology
Function and homology information


histidine decarboxylase / histidine decarboxylase activity / L-histidine metabolic process
Similarity search - Function
Pyruvoyl-Dependent Histidine Decarboxylas; Chain A / Pyruvoyl-Dependent Histidine Decarboxylas, subunit A / Histidine decarboxylase proenzyme / Histidine decarboxylase proenzyme, N-terminal / Histidine carboxylase PI chain / Pyruvoyl-Dependent Histidine Decarboxylase, subunit B / Pyruvoyl-dependent histidine/arginine decarboxylase / Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain / Pyruvoyl-Dependent Histidine Decarboxylase; Chain B / 3-Layer(bba) Sandwich ...Pyruvoyl-Dependent Histidine Decarboxylas; Chain A / Pyruvoyl-Dependent Histidine Decarboxylas, subunit A / Histidine decarboxylase proenzyme / Histidine decarboxylase proenzyme, N-terminal / Histidine carboxylase PI chain / Pyruvoyl-Dependent Histidine Decarboxylase, subunit B / Pyruvoyl-dependent histidine/arginine decarboxylase / Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain / Pyruvoyl-Dependent Histidine Decarboxylase; Chain B / 3-Layer(bba) Sandwich / Few Secondary Structures / Irregular / Alpha Beta
Similarity search - Domain/homology
Histidine decarboxylase proenzyme
Similarity search - Component
Biological speciesLactobacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWorley, S. / Schelp, E. / Monzingo, A.F. / Ernst, S. / Robertus, J.D.
CitationJournal: Proteins / Year: 2002
Title: Structure and cooperativity of a T-state mutant of histidine decarboxylase from Lactobacillus 30a.
Authors: Worley, S. / Schelp, E. / Monzingo, A.F. / Ernst, S. / Robertus, J.D.
History
DepositionMar 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTIDINE DECARBOXYLASE BETA CHAIN
B: HISTIDINE DECARBOXYLASE ALPHA CHAIN
C: HISTIDINE DECARBOXYLASE BETA CHAIN
D: HISTIDINE DECARBOXYLASE ALPHA CHAIN
E: HISTIDINE DECARBOXYLASE BETA CHAIN
F: HISTIDINE DECARBOXYLASE ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)102,4036
Polymers102,4036
Non-polymers00
Water95553
1
A: HISTIDINE DECARBOXYLASE BETA CHAIN
B: HISTIDINE DECARBOXYLASE ALPHA CHAIN
C: HISTIDINE DECARBOXYLASE BETA CHAIN
D: HISTIDINE DECARBOXYLASE ALPHA CHAIN
E: HISTIDINE DECARBOXYLASE BETA CHAIN
F: HISTIDINE DECARBOXYLASE ALPHA CHAIN

A: HISTIDINE DECARBOXYLASE BETA CHAIN
B: HISTIDINE DECARBOXYLASE ALPHA CHAIN
C: HISTIDINE DECARBOXYLASE BETA CHAIN
D: HISTIDINE DECARBOXYLASE ALPHA CHAIN
E: HISTIDINE DECARBOXYLASE BETA CHAIN
F: HISTIDINE DECARBOXYLASE ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)204,80512
Polymers204,80512
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29050 Å2
ΔGint-141 kcal/mol
Surface area31080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.200, 115.309, 202.386
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a hexamer generated by applying a crystallographic two-fold to the trimer in the asymmetric unit: -x, y, -z + 1/2

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Components

#1: Protein HISTIDINE DECARBOXYLASE BETA CHAIN / PI CHAIN


Mass: 8848.862 Da / Num. of mol.: 3 / Fragment: BETA CHAIN (RESIDUES 1-81) / Mutation: D53N, D54N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus sp. (bacteria) / Strain: 30A / Gene: HDCA / Production host: Escherichia coli (E. coli) / References: UniProt: P00862, histidine decarboxylase
#2: Protein HISTIDINE DECARBOXYLASE ALPHA CHAIN


Mass: 25285.375 Da / Num. of mol.: 3 / Fragment: ALPHA CHAIN (RESIDUES 82-310)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus sp. (bacteria) / Strain: 30A / Gene: HDCA / Production host: Escherichia coli (E. coli) / References: UniProt: P00862, histidine decarboxylase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 400, PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
20-15 %PEG4001reservoir
34-8 %PEG40001reservoir
40.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 1999
RadiationMonochromator: DOUBLE FOCUSSING MIRRORS (NI & PT) + NI FILTER
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.58→100 Å / Num. all: 34308 / Num. obs: 34308 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 57.2 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.1
Reflection shellResolution: 2.58→2.67 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.389 / % possible all: 90.5
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 100 Å / Redundancy: 2.7 %
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PYA

1pya


Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.316 2843 RANDOM
Rwork0.2597 --
obs0.266 28602 -
all-34112 -
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7119 0 0 53 7172
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg3.4
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 3 / Rfactor Rfree: 0.317
Solvent computation
*PLUS
Displacement parameters
*PLUS

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