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- PDB-4zgz: STRUCTURE OF HUMAN ANTIZYME INHIBITOR IN COMPLEX WITH A C-TERMINA... -

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Basic information

Entry
Database: PDB / ID: 4zgz
TitleSTRUCTURE OF HUMAN ANTIZYME INHIBITOR IN COMPLEX WITH A C-TERMINAL FRAGMENT OF ANTIZYME
Components
  • Antizyme inhibitor 1
  • Ornithine decarboxylase antizyme 1
KeywordsPROTEIN BINDING / TIM BARREL DOMAIN / BETA-SHEET DOMAIN / INHIBITION / ANTIZYME / PLASMA
Function / homology
Function and homology information


ornithine decarboxylase activator activity / positive regulation of polyamine transmembrane transport / negative regulation of polyamine transmembrane transport / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / polyamine biosynthetic process / positive regulation of intracellular protein transport / Regulation of ornithine decarboxylase (ODC) / regulation of cellular amino acid metabolic process / ornithine decarboxylase inhibitor activity ...ornithine decarboxylase activator activity / positive regulation of polyamine transmembrane transport / negative regulation of polyamine transmembrane transport / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / polyamine biosynthetic process / positive regulation of intracellular protein transport / Regulation of ornithine decarboxylase (ODC) / regulation of cellular amino acid metabolic process / ornithine decarboxylase inhibitor activity / negative regulation of protein catabolic process / positive regulation of protein catabolic process / nucleus / cytoplasm / cytosol
Similarity search - Function
Antizyme inhibitor 1 / Ornithine decarboxylase antizyme / Ornithine decarboxylase antizyme superfamily / Ornithine decarboxylase antizyme / Ornithine decarboxylase antizyme signature. / Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain ...Antizyme inhibitor 1 / Ornithine decarboxylase antizyme / Ornithine decarboxylase antizyme superfamily / Ornithine decarboxylase antizyme / Ornithine decarboxylase antizyme signature. / Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved 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 / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Antizyme inhibitor 1 / Ornithine decarboxylase antizyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.81 Å
AuthorsChen, S.F. / Wu, H.Y. / Chan, N.L.
Funding support Taiwan, 5items
OrganizationGrant numberCountry
Ministry of Science and TechnologyNSC99-2113-M-002-008-MY3 Taiwan
Ministry of Science and TechnologyNSC101-2911-I-002-303- Taiwan
National Research Program for BiopharmaceuticalsNSC101-2325-B-002-049 Taiwan
National Taiwan UniversityNTU-102-027-MY3 Taiwan
National Taiwan UniversityNTU-103-008-MY3 Taiwan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis of antizyme-mediated regulation of polyamine homeostasis
Authors: Wu, H.Y. / Chen, S.F. / Hsieh, J.Y. / Chou, F. / Wang, Y.H. / Lin, W.T. / Lee, P.Y. / Yu, Y.J. / Lin, L.Y. / Lin, T.S. / Lin, C.L. / Liu, G.Y. / Tzeng, S.R. / Hung, H.C. / Chan, N.L.
History
DepositionApr 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Nov 8, 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 / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antizyme inhibitor 1
B: Ornithine decarboxylase antizyme 1
C: Antizyme inhibitor 1
D: Ornithine decarboxylase antizyme 1


Theoretical massNumber of molelcules
Total (without water)126,4994
Polymers126,4994
Non-polymers00
Water00
1
A: Antizyme inhibitor 1
B: Ornithine decarboxylase antizyme 1


Theoretical massNumber of molelcules
Total (without water)63,2502
Polymers63,2502
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-17 kcal/mol
Surface area24260 Å2
MethodPISA
2
C: Antizyme inhibitor 1
D: Ornithine decarboxylase antizyme 1


Theoretical massNumber of molelcules
Total (without water)63,2502
Polymers63,2502
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-15 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.563, 166.563, 144.864
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Antizyme inhibitor 1 / AZI / Ornithine decarboxylase antizyme inhibitor


Mass: 48470.836 Da / Num. of mol.: 2
Fragment: HUMAN ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR, UNP residues 2-437
Mutation: N21D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AZIN1, OAZI, OAZIN / Plasmid: 28B-HAZIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: O14977
#2: Protein Ornithine decarboxylase antizyme 1 / ODC-Az


Mass: 14778.683 Da / Num. of mol.: 2
Fragment: HUMAN ORNITHINE DECARBOXYLASE ANTIZYME, UNP residues 110-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAZ1, OAZ / Plasmid: 21B-AZ110 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: P54368
Sequence detailsTHE SEQUENCE CONFLICT ASN20ASP BASED ON REFERENCE 1 OF DATABASE UNIPORT O14977.

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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: 9.17 Å3/Da / Density % sol: 86.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M N-(2-ACETAMIDO)IMINODIACETIC ACID (ADA) PH 6.5, 1.0M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2012
RadiationMonochromator: LN2-COOLED, FIXED-EXIT DOUBLE CRYSTAL MONOCHROMATOR(CRYSTAL TYPE SI(111))
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 5.8→30 Å / Num. obs: 12070 / % possible obs: 97.1 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rsym value: 0.048 / Net I/σ(I): 11
Reflection shellResolution: 5.84→6.29 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIX(PHENIX.REFINE:1.7.3_928)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BTN

3btn


Resolution: 5.81→25.92 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.8 / Stereochemistry target values: ML
Details: DUE TO THE LOW RESOLUTION NATURE OF THIS STRUCTURE, SEQUENCE ASSIGNMENT AND SIDE CHAIN MODELING WERE GUIDED BY REFERRING TO THE HIGH RESOLUTION STRUCTURES OF HUMAN ANTIZYME (PDBID: 4ZGY) AND ...Details: DUE TO THE LOW RESOLUTION NATURE OF THIS STRUCTURE, SEQUENCE ASSIGNMENT AND SIDE CHAIN MODELING WERE GUIDED BY REFERRING TO THE HIGH RESOLUTION STRUCTURES OF HUMAN ANTIZYME (PDBID: 4ZGY) AND MOUSE ANTIZYME INHIBITOR (PDBID: 3BTN). REFINING THESE SIDE CHAIN ATOMS WOULD BE UNREALISTIC AT 5.8A RESOLUTION AND THUS THEIR OCCUPANCIES WERE SET TO ZERO.
RfactorNum. reflection% reflection
Rfree0.24 593 4.93 %
Rwork0.188 --
obs0.191 12031 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.81→25.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7456 0 0 0 7456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037630
X-RAY DIFFRACTIONf_angle_d0.84910337
X-RAY DIFFRACTIONf_dihedral_angle_d11.8082697
X-RAY DIFFRACTIONf_chiral_restr0.0541159
X-RAY DIFFRACTIONf_plane_restr0.0031318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.8123-6.38920.26411420.21652906X-RAY DIFFRACTION99
6.3892-7.29570.20811580.16862892X-RAY DIFFRACTION100
7.2957-9.12470.20161450.18052897X-RAY DIFFRACTION99
9.1247-25.92210.25981480.19092743X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -40.7491 Å / Origin y: 122.8579 Å / Origin z: 13.7624 Å
111213212223313233
T0.2842 Å2-0.0354 Å2-0.0315 Å2-0.7541 Å2-0.0265 Å2--0.2438 Å2
L1.4202 °2-0.8881 °20.2887 °2-1.1363 °20.1943 °2--0.4208 °2
S-0.4291 Å °-0.2468 Å °-0.2258 Å °0.6931 Å °0.0376 Å °0.3722 Å °0.0817 Å °0.007 Å °-0.2056 Å °
Refinement TLS groupSelection details: all

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