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- PDB-1rz0: Flavin reductase PheA2 in native state -

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Basic information

Entry
Database: PDB / ID: 1rz0
TitleFlavin reductase PheA2 in native state
Componentsphenol 2-hydroxylase component B
KeywordsOXIDOREDUCTASE / flavin / FAD
Function / homology
Function and homology information


pyrimidine nucleobase catabolic process / riboflavin reductase (NADPH) activity / FMN binding
Similarity search - Function
: / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Phenol 2-hydroxylase component B
Similarity search - Component
Biological speciesGeobacillus thermoglucosidasius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
Authorsvan den Heuvel, R.H. / Westphal, A.H. / Heck, A.J. / Walsh, M.A. / Rovida, S. / van Berkel, W.J. / Mattevi, A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Studies on Flavin Reductase PheA2 Reveal Binding of NAD in an Unusual Folded Conformation and Support Novel Mechanism of Action.
Authors: Van Den Heuvel, R.H. / Westphal, A.H. / Heck, A.J. / Walsh, M.A. / Rovida, S. / Van Berkel, W.J. / Mattevi, A.
History
DepositionDec 23, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: phenol 2-hydroxylase component B
B: phenol 2-hydroxylase component B
C: phenol 2-hydroxylase component B
D: phenol 2-hydroxylase component B
E: phenol 2-hydroxylase component B
F: phenol 2-hydroxylase component B
G: phenol 2-hydroxylase component B
H: phenol 2-hydroxylase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,94616
Polymers143,6618
Non-polymers6,2848
Water7,332407
1
A: phenol 2-hydroxylase component B
B: phenol 2-hydroxylase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4864
Polymers35,9152
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-60 kcal/mol
Surface area13250 Å2
MethodPISA
2
C: phenol 2-hydroxylase component B
D: phenol 2-hydroxylase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4864
Polymers35,9152
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-61 kcal/mol
Surface area13220 Å2
MethodPISA
3
E: phenol 2-hydroxylase component B
F: phenol 2-hydroxylase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4864
Polymers35,9152
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-61 kcal/mol
Surface area13260 Å2
MethodPISA
4
G: phenol 2-hydroxylase component B
H: phenol 2-hydroxylase component B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4864
Polymers35,9152
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-60 kcal/mol
Surface area13250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.544, 154.268, 83.866
Angle α, β, γ (deg.)90.00, 91.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91A
101B
111C
121D
131E
141F
151G
161H
171A
181B
191C
201D
211E
221F
231G
241H

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLYGLYAA3 - 843 - 84
21ASPASPGLYGLYBB3 - 843 - 84
31ASPASPGLYGLYCC3 - 843 - 84
41ASPASPGLYGLYDD3 - 843 - 84
51ASPASPGLYGLYEE3 - 843 - 84
61ASPASPGLYGLYFF3 - 843 - 84
71ASPASPGLYGLYGG3 - 843 - 84
81ASPASPGLYGLYHH3 - 843 - 84
92ASPASPGLNGLNAA91 - 15391 - 153
102ASPASPGLNGLNBB91 - 15391 - 153
112ASPASPGLNGLNCC91 - 15391 - 153
122ASPASPGLNGLNDD91 - 15391 - 153
132ASPASPGLNGLNEE91 - 15391 - 153
142ASPASPGLNGLNFF91 - 15391 - 153
152ASPASPGLNGLNGG91 - 15391 - 153
162ASPASPGLNGLNHH91 - 15391 - 153
173FADFADFADFADAI1200
183FADFADFADFADBJ2200
193FADFADFADFADCK3200
203FADFADFADFADDL4200
213FADFADFADFADEM5200
223FADFADFADFADFN6200
233FADFADFADFADGO7200
243FADFADFADFADHP8200

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Components

#1: Protein
phenol 2-hydroxylase component B / Flavin reductase PheA2


Mass: 17957.650 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermoglucosidasius (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q9LAG2
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.42 Å3/Da / Density % sol: 48.68 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.88570, 0.97917
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 12, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.88571
20.979171
ReflectionResolution: 2.2→15 Å / Num. obs: 66610 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
MAR345data collection
CCP4(SCALA)data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.264 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25277 1322 2 %RANDOM
Rwork0.22153 ---
all0.22217 ---
obs0.22217 64114 95.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.059 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å2-0.21 Å2
2--1.03 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9408 0 424 407 10239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210000
X-RAY DIFFRACTIONr_angle_refined_deg1.4432.01813568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54651216
X-RAY DIFFRACTIONr_chiral_restr0.090.21576
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027144
X-RAY DIFFRACTIONr_nbd_refined0.2040.24665
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2506
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5180.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.217
X-RAY DIFFRACTIONr_mcbond_it0.7151.56056
X-RAY DIFFRACTIONr_mcangle_it1.41529760
X-RAY DIFFRACTIONr_scbond_it2.38133944
X-RAY DIFFRACTIONr_scangle_it3.7694.53808
Refine LS restraints NCS

Ens-ID: 1 / Number: 1164 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.050.05
3Ctight positional0.040.05
4Dtight positional0.040.05
5Etight positional0.040.05
6Ftight positional0.040.05
7Gtight positional0.040.05
8Htight positional0.050.05
1Atight thermal0.140.5
2Btight thermal0.140.5
3Ctight thermal0.130.5
4Dtight thermal0.130.5
5Etight thermal0.130.5
6Ftight thermal0.140.5
7Gtight thermal0.140.5
8Htight thermal0.140.5
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 78
Rwork0.269 4628

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