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- PDB-1j0b: Crystal Structure Analysis of the ACC deaminase homologue complex... -

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Basic information

Entry
Database: PDB / ID: 1j0b
TitleCrystal Structure Analysis of the ACC deaminase homologue complexed with inhibitor
Components1-aminocyclopropane-1-carboxylate deaminase
KeywordsLYASE / PLP dependent
Function / homology
Function and homology information


1-aminocyclopropane-1-carboxylate deaminase / 1-aminocyclopropane-1-carboxylate deaminase activity
Similarity search - Function
D-cysteine desulfhydrase / 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5PA / Putative 1-aminocyclopropane-1-carboxylate deaminase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFujino, A. / Ose, T. / Honma, M. / Yao, M. / Tanaka, I.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural and enzymatic properties of 1-aminocyclopropane-1-carboxylate deaminase homologue from Pyrococcus horikoshii
Authors: Fujino, A. / Ose, T. / Yao, M. / Tokiwano, T. / Honma, M. / Watanabe, N. / Tanaka, I.
History
DepositionNov 12, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 13, 2014Group: Structure summary
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
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_asym_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_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

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Assembly

Deposited unit
A: 1-aminocyclopropane-1-carboxylate deaminase
B: 1-aminocyclopropane-1-carboxylate deaminase
C: 1-aminocyclopropane-1-carboxylate deaminase
D: 1-aminocyclopropane-1-carboxylate deaminase
E: 1-aminocyclopropane-1-carboxylate deaminase
F: 1-aminocyclopropane-1-carboxylate deaminase
G: 1-aminocyclopropane-1-carboxylate deaminase
H: 1-aminocyclopropane-1-carboxylate deaminase
I: 1-aminocyclopropane-1-carboxylate deaminase
J: 1-aminocyclopropane-1-carboxylate deaminase
K: 1-aminocyclopropane-1-carboxylate deaminase
L: 1-aminocyclopropane-1-carboxylate deaminase
M: 1-aminocyclopropane-1-carboxylate deaminase
N: 1-aminocyclopropane-1-carboxylate deaminase
O: 1-aminocyclopropane-1-carboxylate deaminase
P: 1-aminocyclopropane-1-carboxylate deaminase
Q: 1-aminocyclopropane-1-carboxylate deaminase
R: 1-aminocyclopropane-1-carboxylate deaminase
S: 1-aminocyclopropane-1-carboxylate deaminase
T: 1-aminocyclopropane-1-carboxylate deaminase
U: 1-aminocyclopropane-1-carboxylate deaminase
V: 1-aminocyclopropane-1-carboxylate deaminase
W: 1-aminocyclopropane-1-carboxylate deaminase
X: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)853,56248
Polymers845,58824
Non-polymers7,97424
Water14,484804
1
A: 1-aminocyclopropane-1-carboxylate deaminase
B: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1304
Polymers70,4662
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-27 kcal/mol
Surface area22930 Å2
MethodPISA
2
C: 1-aminocyclopropane-1-carboxylate deaminase
D: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1304
Polymers70,4662
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-27 kcal/mol
Surface area22900 Å2
MethodPISA
3
E: 1-aminocyclopropane-1-carboxylate deaminase
F: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1304
Polymers70,4662
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-28 kcal/mol
Surface area23170 Å2
MethodPISA
4
G: 1-aminocyclopropane-1-carboxylate deaminase
H: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1304
Polymers70,4662
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-25 kcal/mol
Surface area23030 Å2
MethodPISA
5
I: 1-aminocyclopropane-1-carboxylate deaminase
J: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1304
Polymers70,4662
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-26 kcal/mol
Surface area23010 Å2
MethodPISA
6
K: 1-aminocyclopropane-1-carboxylate deaminase
L: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1304
Polymers70,4662
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-27 kcal/mol
Surface area22880 Å2
MethodPISA
7
M: 1-aminocyclopropane-1-carboxylate deaminase
N: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1304
Polymers70,4662
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-28 kcal/mol
Surface area23000 Å2
MethodPISA
8
O: 1-aminocyclopropane-1-carboxylate deaminase
P: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1304
Polymers70,4662
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-27 kcal/mol
Surface area23010 Å2
MethodPISA
9
Q: 1-aminocyclopropane-1-carboxylate deaminase
R: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1304
Polymers70,4662
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-27 kcal/mol
Surface area23050 Å2
MethodPISA
10
S: 1-aminocyclopropane-1-carboxylate deaminase
T: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1304
Polymers70,4662
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-28 kcal/mol
Surface area23160 Å2
MethodPISA
11
U: 1-aminocyclopropane-1-carboxylate deaminase
V: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1304
Polymers70,4662
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-28 kcal/mol
Surface area22950 Å2
MethodPISA
12
W: 1-aminocyclopropane-1-carboxylate deaminase
X: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1304
Polymers70,4662
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-27 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.87, 147.28, 149.07
Angle α, β, γ (deg.)73.18, 90.11, 68.49
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
1-aminocyclopropane-1-carboxylate deaminase / / ACC / ACC deaminase


Mass: 35232.824 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O57809, EC: 4.1.99.4
#2: Chemical...
ChemComp-5PA / N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-Y-LMETHYL]-1-AMINO-CYCLOPROPANECARBOXYLIC ACID / N-PYRIDOXYL-1-AMINO-CYCLOPROPANECARBOXYLIC ACID-5-MONOPHOSPHATE


Mass: 332.246 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C12H17N2O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, 2-propanol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 277 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMpotassium phosphate1droppH7.0
210 mg/mlprotein1drop
30.1 MACC1drop
40.1 MTris1drop
50.045 Mpotassium phosphate1droppH8.5
60.1 Msodium HEPES1reservoirpH7.5
710 %(w/v)2-propanol1reservoir
813-15 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 19, 2001 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 245565 / Num. obs: 244791 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 58.82 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.047 / Net I/σ(I): 7.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.2 / Num. unique all: 35772 / Rsym value: 0.276 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 39.1 Å / % possible obs: 100 % / Num. measured all: 244791
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 100 % / Num. unique obs: 35772 / Num. measured obs: 87298

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.342 17821 -RANDOM
Rwork0.291 ---
all-214317 --
obs-214269 100 %-
Displacement parametersBiso mean: 52.687 Å2
Baniso -1Baniso -2Baniso -3
1--1.017 Å22.246 Å2-3.401 Å2
2--2.886 Å28.244 Å2
3----1.869 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59616 0 528 804 60948
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0191
X-RAY DIFFRACTIONc_angle_deg1.972
X-RAY DIFFRACTIONc_dihedral_angle_d22.9624
X-RAY DIFFRACTIONc_improper_angle_d1.168
LS refinement shellResolution: 2.7→2.79 Å
RfactorNum. reflection% reflection
Rfree0.435 1785 -
Rwork0.429 --
obs-21352 99.77 %
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 8 % / Rfactor Rfree: 0.32 / Rfactor Rwork: 0.2918
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.973
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.96
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.168

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