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- PDB-8hm9: X-ray Crystal Structure of Pseudoazurin Met16His Variant at pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 8hm9
TitleX-ray Crystal Structure of Pseudoazurin Met16His Variant at pH 4.0
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT / electron transfer protein
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Pseudoazurin
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsAoyama, Y. / Yamaguchi, T. / Kohzuma, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: To Be Published
Title: X-ray Crystal Structure of Pseudoazurin Met16His Variant at pH 4.0
Authors: Aoyama, Y. / Yamaguchi, T. / Kohzuma, T.
History
DepositionDec 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pseudoazurin
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2074
Polymers26,0802
Non-polymers1272
Water7,260403
1
A: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1032
Polymers13,0401
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1032
Polymers13,0401
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.196, 60.476, 54.865
Angle α, β, γ (deg.)90.000, 105.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pseudoazurin / Blue copper protein


Mass: 13039.892 Da / Num. of mol.: 2 / Mutation: M16H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: bcp / Production host: Escherichia coli (E. coli) / References: UniProt: P19567
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 31% PEG1500, 0.1 M potassium phosphate (pH 4.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.052 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.052 Å / Relative weight: 1
ReflectionResolution: 1.36→39.77 Å / Num. obs: 47237 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.039 / Rrim(I) all: 0.058 / Net I/σ(I): 13.6
Reflection shellResolution: 1.36→1.38 Å / Redundancy: 3 % / Rmerge(I) obs: 0.267 / Num. unique obs: 2344 / CC1/2: 0.884 / Rpim(I) all: 0.247 / Rrim(I) all: 0.365

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YL4

4yl4


Resolution: 1.36→39.77 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.37 / SU ML: 0.042 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1603 2207 4.674 %
Rwork0.1279 45009 -
all0.129 --
obs-47216 99.245 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.552 Å2
Baniso -1Baniso -2Baniso -3
1-0.172 Å2-0 Å21.725 Å2
2---2.427 Å2-0 Å2
3---1.101 Å2
Refinement stepCycle: LAST / Resolution: 1.36→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 2 403 2235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121978
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161918
X-RAY DIFFRACTIONr_angle_refined_deg1.651.6542691
X-RAY DIFFRACTIONr_angle_other_deg0.5421.5874464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9485270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.63752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38310339
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.0841074
X-RAY DIFFRACTIONr_chiral_restr0.0910.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_nbd_refined0.2170.2326
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21634
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2921
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21024
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2233
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3430.211
X-RAY DIFFRACTIONr_nbd_other0.2430.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1910.251
X-RAY DIFFRACTIONr_mcbond_it1.2611.5361050
X-RAY DIFFRACTIONr_mcbond_other1.2611.5351050
X-RAY DIFFRACTIONr_mcangle_it1.6132.7681330
X-RAY DIFFRACTIONr_mcangle_other1.6132.7751331
X-RAY DIFFRACTIONr_scbond_it1.4581.799928
X-RAY DIFFRACTIONr_scbond_other1.4591.804929
X-RAY DIFFRACTIONr_scangle_it1.8593.161361
X-RAY DIFFRACTIONr_scangle_other1.8583.1651362
X-RAY DIFFRACTIONr_lrange_it3.63924.8242236
X-RAY DIFFRACTIONr_lrange_other2.9218.472085
X-RAY DIFFRACTIONr_rigid_bond_restr5.01433896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.3950.1871680.1613343X-RAY DIFFRACTION99.8578
1.395-1.4330.1981650.1563246X-RAY DIFFRACTION99.9414
1.433-1.4750.2021550.1453173X-RAY DIFFRACTION99.88
1.475-1.520.1771440.1223048X-RAY DIFFRACTION99.8436
1.52-1.570.1611490.1172986X-RAY DIFFRACTION99.7455
1.57-1.6250.1451230.122893X-RAY DIFFRACTION99.6695
1.625-1.6860.1611300.1112768X-RAY DIFFRACTION99.7247
1.686-1.7550.171390.1152665X-RAY DIFFRACTION99.822
1.755-1.8330.2061200.122548X-RAY DIFFRACTION99.3299
1.833-1.9220.1781050.1212451X-RAY DIFFRACTION99.3007
1.922-2.0260.1431220.1212308X-RAY DIFFRACTION98.7002
2.026-2.1480.1561180.1212168X-RAY DIFFRACTION98.7047
2.148-2.2960.1571040.1132061X-RAY DIFFRACTION98.7232
2.296-2.480.1551060.1221898X-RAY DIFFRACTION98.4283
2.48-2.7150.165990.1221767X-RAY DIFFRACTION98.2105
2.715-3.0340.15650.1261602X-RAY DIFFRACTION98.2322
3.034-3.50.133650.1341417X-RAY DIFFRACTION97.5642
3.5-4.2780.145650.1271173X-RAY DIFFRACTION97.6341
4.278-6.0160.162450.145938X-RAY DIFFRACTION98.3984
6.016-39.770.179200.179556X-RAY DIFFRACTION98.9691

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