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- PDB-5c2i: Crystal structure of Anabaena sp. DyP-type peroxidese (AnaPX) -

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Basic information

Entry
Database: PDB / ID: 5c2i
TitleCrystal structure of Anabaena sp. DyP-type peroxidese (AnaPX)
ComponentsAlr1585 protein
KeywordsOXIDOREDUCTASE / DyP-type peroxidase / Dye-decolorizing peroxidase
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
ACETIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Alr1585 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsYoshida, T. / Amano, Y. / Tsuge, H. / Sugano, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS26450132 Japan
CitationJournal: Proteins / Year: 2016
Title: Anabaena sp. DyP-type peroxidase is a tetramer consisting of two asymmetric dimers.
Authors: Yoshida, T. / Ogola, H.J. / Amano, Y. / Hisabori, T. / Ashida, H. / Sawa, Y. / Tsuge, H. / Sugano, Y.
History
DepositionJun 16, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alr1585 protein
B: Alr1585 protein
C: Alr1585 protein
D: Alr1585 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,94216
Polymers213,8314
Non-polymers3,11112
Water17,222956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14180 Å2
ΔGint-94 kcal/mol
Surface area69810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.734, 132.601, 176.528
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 2 - 469 / Label seq-ID: 1 - 468

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
Alr1585 protein


Mass: 53457.867 Da / Num. of mol.: 4 / Mutation: D204H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / UTEX 2576) (bacteria)
Strain: PCC 7120 / UTEX 2576 / Gene: alr1585 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8YWM0

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Non-polymers , 5 types, 968 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 956 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 7, 2011
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 207238 / % possible obs: 90.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.06882 / Net I/σ(I): 17.62
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.4 % / % possible all: 81.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREP11.1.03phasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G2C

4g2c


Resolution: 1.89→34.73 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.187 / WRfactor Rwork: 0.171 / SU B: 4.957 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 9114 5 %RANDOM
Rwork0.1808 172763 --
obs0.1817 172799 91.81 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 80.04 Å2 / Biso mean: 29.286 Å2 / Biso min: 6.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2--1.17 Å20 Å2
3----0.43 Å2
Refinement stepCycle: final / Resolution: 1.89→34.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14941 0 214 956 16111
Biso mean--20.48 30.13 -
Num. residues----1850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915542
X-RAY DIFFRACTIONr_bond_other_d0.0070.0214507
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.96221068
X-RAY DIFFRACTIONr_angle_other_deg1.254333348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88651843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47524.689821
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.612152619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9971596
X-RAY DIFFRACTIONr_chiral_restr0.0930.22170
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02117952
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023830
X-RAY DIFFRACTIONr_mcbond_it0.991.3557394
X-RAY DIFFRACTIONr_mcbond_other0.991.3557392
X-RAY DIFFRACTIONr_mcangle_it1.5542.0259229
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A285180.1
12B285180.1
21A288490.1
22C288490.1
31A291730.08
32D291730.08
41B291320.08
42C291320.08
51B285050.1
52D285050.1
61C286630.1
62D286630.1
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.89-1.9390.266240.249113141448282.4330.212
1.939-1.9920.2545920.244111271414782.8370.203
1.992-2.050.2445780.22109371371883.9410.185
2.05-2.1130.2255360.213109181342185.3440.181
2.113-2.1820.2335860.201106861292887.1910.168
2.182-2.2580.2295620.196105671254688.7060.166
2.258-2.3430.2185680.195104421211890.8570.158
2.343-2.4390.2325380.193102771165392.8090.158
2.439-2.5470.2095490.187100571125694.2250.155
2.547-2.6710.2015160.1997771070396.1690.159
2.671-2.8150.2094770.18794431023596.9220.163
2.815-2.9850.2074720.1829053968998.3070.165
2.985-3.190.2094600.1848548910198.9780.171
3.19-3.4450.1983920.1798081852899.3550.175
3.445-3.7720.1853770.1817450786399.5420.184
3.772-4.2140.1673870.1546707712699.5510.162
4.214-4.860.1553260.1395958632699.3360.153
4.86-5.9390.1872370.1695162541099.7970.187
5.939-8.340.1742120.1584028425999.5540.178
8.34-50.0050.1761250.1872190252291.7920.219
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)
10.7470.27040.24150.81030.29530.88530.0384-0.0477-0.04850.0246-0.00990.0132-0.0135-0.036-0.02850.0637-0.0125-0.00190.01690.01380.075-29.252-19.386-27.488
21.16810.14880.00170.8576-0.07950.75950.0664-0.0909-0.04420.1192-0.0644-0.1734-0.0320.0818-0.0020.1262-0.0068-0.10840.05060.0130.195813.508-15.754-12.527
30.83360.13290.04940.9192-0.12960.6808-0.02780.1115-0.0385-0.0713-0.0106-0.00160.0560.09520.03830.1344-0.0496-0.02720.09760.01340.0428-18.195-2.866-69.414
40.51870.01630.04141.098-0.36661.04070.01720.0875-0.0565-0.10560.0319-0.26310.070.0867-0.04910.07350.010.04610.0983-0.00760.255624.921-6.394-56.569
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 469
2X-RAY DIFFRACTION2B2 - 469
3X-RAY DIFFRACTION3C2 - 469
4X-RAY DIFFRACTION4D2 - 469

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