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- PDB-2iiz: Crystal structure of putative melanin biosynthesis protein TyrA w... -

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Basic information

Entry
Database: PDB / ID: 2iiz
TitleCrystal structure of putative melanin biosynthesis protein TyrA with bound heme (NP_716371.1) from Shewanella Oneidensis at 2.30 A resolution
ComponentsMelanin biosynthesis protein TyrA, putative
KeywordsStructural Genomics/Unknown function / NP_716371.1 / putative melanin biosynthesis protein TyrA / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / Structural Genomics-Unknown function COMPLEX
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / ISOPROPYL ALCOHOL / Dyp-type heme-dependent peroxidase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2007
Title: Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA.
Authors: Zubieta, C. / Joseph, R. / Krishna, S.S. / McMullan, D. / Kapoor, M. / Axelrod, H.L. / Miller, M.D. / Abdubek, P. / Acosta, C. / Astakhova, T. / Carlton, D. / Chiu, H.J. / Clayton, T. / ...Authors: Zubieta, C. / Joseph, R. / Krishna, S.S. / McMullan, D. / Kapoor, M. / Axelrod, H.L. / Miller, M.D. / Abdubek, P. / Acosta, C. / Astakhova, T. / Carlton, D. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Elias, Y. / Elsliger, M.A. / Feuerhelm, J. / Grzechnik, S.K. / Hale, J. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Kumar, A. / Marciano, D. / Morse, A.T. / Murphy, K.D. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Reyes, R. / Rife, C.L. / Schimmel, P. / Trout, C.V. / van den Bedem, H. / Weekes, D. / White, A. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionSep 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). STATIC LIGHT SCATTERING AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY MEASUREMENTS INDICATE THAT THE PROTEIN IS A DIMER IN SOLUTION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Melanin biosynthesis protein TyrA, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2946
Polymers36,4701
Non-polymers8245
Water2,018112
1
A: Melanin biosynthesis protein TyrA, putative
hetero molecules

A: Melanin biosynthesis protein TyrA, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,58712
Polymers72,9402
Non-polymers1,64710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)94.837, 94.837, 116.666
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Melanin biosynthesis protein TyrA, putative


Mass: 36469.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: NP_716371.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EIU4

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Non-polymers , 5 types, 117 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.58 Å3/Da / Density % sol: 65.41 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 5% isopropyl alcohol, 20% (w/v) polyethylene glycol 4000, additive - 1mM hemin, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→19.9 Å / Num. obs: 24210 / % possible obs: 99.7 % / Redundancy: 6.95 % / Biso Wilson estimate: 38.592 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 11.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allΧ2% possible all
2.3-2.450.55232918640947.1100
2.45-2.680.5213.43329546667.1100
2.68-2.990.4324.93001242367.199.9
2.99-3.450.2219.7266923835799.8
3.45-4.220.08720.82218132826.899.8
4.22-5.950.05329.41711226016.699.6
5.95-19.90.03235.3978714926.696.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.2.0005refinement
MolProbity3beta29model building
PDB_EXTRACT2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HAG

2hag


Resolution: 2.3→19.8 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.526 / SU ML: 0.18 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.70 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RESIDUES 1-5 AND 311 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 5. THE PROTEIN WAS CO- CRYSTALLIZED IN THE PRESENCE OF FE PROTOPORPHYRIN (IX).
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1269 5.2 %RANDOM
Rwork0.205 ---
obs0.208 24207 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.304 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20 Å2
2---1.39 Å20 Å2
3---2.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 0 56 112 2609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222566
X-RAY DIFFRACTIONr_bond_other_d0.0020.022221
X-RAY DIFFRACTIONr_angle_refined_deg1.3572.0013474
X-RAY DIFFRACTIONr_angle_other_deg0.76335160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04924.254134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86915421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2741516
X-RAY DIFFRACTIONr_chiral_restr0.0760.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022888
X-RAY DIFFRACTIONr_gen_planes_other00.02530
X-RAY DIFFRACTIONr_nbd_refined0.2030.2567
X-RAY DIFFRACTIONr_nbd_other0.190.22213
X-RAY DIFFRACTIONr_nbtor_refined0.180.21217
X-RAY DIFFRACTIONr_nbtor_other0.0870.21358
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2107
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2920.29
X-RAY DIFFRACTIONr_mcbond_it1.3331525
X-RAY DIFFRACTIONr_mcbond_other0.3293621
X-RAY DIFFRACTIONr_mcangle_it2.28152446
X-RAY DIFFRACTIONr_scbond_it4.38781075
X-RAY DIFFRACTIONr_scangle_it5.78111027
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 88 -
Rwork0.292 1650 -
obs-1738 99.94 %
Refinement TLS params.Method: refined / Origin x: -19.721 Å / Origin y: -19.058 Å / Origin z: -18.559 Å
111213212223313233
T0.0566 Å2-0.0344 Å20.0412 Å2--0.0962 Å20.0093 Å2---0.1493 Å2
L1.7409 °2-0.6528 °20.0518 °2-3.598 °2-0.5402 °2--2.0832 °2
S0.0579 Å °0.3242 Å °0.047 Å °-0.4916 Å °-0.0705 Å °-0.3376 Å °0.113 Å °0.2124 Å °0.0126 Å °
Refinement TLS groupSelection: ALL

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