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- PDB-4n3e: Crystal structure of Hyp-1, a St John's wort PR-10 protein, in co... -

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Entry
Database: PDB / ID: 4n3e
TitleCrystal structure of Hyp-1, a St John's wort PR-10 protein, in complex with 8-anilino-1-naphthalene sulfonate (ANS)
ComponentsPhenolic oxidative coupling protein
KeywordsPLANT PROTEIN / PLANT HORMONE BINDING / PHYTOHORMONE BINDING / CYTOKININ / PLANT DEFENSE / PATHOGENESIS-RELATED PROTEIN / PR-10 PROTEIN / HYPERICIN / DEPRESSION / PR-10 FOLD / HYDROPHOBIC CAVITY / GLYCINE-RICH LOOP / ANS DISPLACEMENT ASSAY (ADA) / COMMENSURATELY MODULATED SUPERSTRUCTURE / TETARTOHEDRAL TWINNING
Function / homology
Function and homology information


response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity
Similarity search - Function
Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
8-ANILINO-1-NAPHTHALENE SULFONATE / Phenolic oxidative coupling protein
Similarity search - Component
Biological speciesHypericum perforatum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsSliwiak, J. / Dauter, Z. / Mccoy, A.J. / Read, R.J. / Jaskolski, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartohedral twinning and sevenfold translational noncrystallographic symmetry.
Authors: Sliwiak, J. / Jaskolski, M. / Dauter, Z. / McCoy, A.J. / Read, R.J.
History
DepositionOct 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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

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Assembly

Deposited unit
A: Phenolic oxidative coupling protein
B: Phenolic oxidative coupling protein
C: Phenolic oxidative coupling protein
D: Phenolic oxidative coupling protein
E: Phenolic oxidative coupling protein
F: Phenolic oxidative coupling protein
G: Phenolic oxidative coupling protein
H: Phenolic oxidative coupling protein
I: Phenolic oxidative coupling protein
J: Phenolic oxidative coupling protein
K: Phenolic oxidative coupling protein
L: Phenolic oxidative coupling protein
M: Phenolic oxidative coupling protein
N: Phenolic oxidative coupling protein
O: Phenolic oxidative coupling protein
P: Phenolic oxidative coupling protein
Q: Phenolic oxidative coupling protein
R: Phenolic oxidative coupling protein
S: Phenolic oxidative coupling protein
T: Phenolic oxidative coupling protein
U: Phenolic oxidative coupling protein
V: Phenolic oxidative coupling protein
W: Phenolic oxidative coupling protein
X: Phenolic oxidative coupling protein
Y: Phenolic oxidative coupling protein
Z: Phenolic oxidative coupling protein
a: Phenolic oxidative coupling protein
b: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)545,269122
Polymers517,86328
Non-polymers27,40694
Water63135
1
A: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6925
Polymers18,4951
Non-polymers1,1974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9926
Polymers18,4951
Non-polymers1,4975
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9316
Polymers18,4951
Non-polymers1,4365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3934
Polymers18,4951
Non-polymers8983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9926
Polymers18,4951
Non-polymers1,4975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7942
Polymers18,4951
Non-polymers2991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9926
Polymers18,4951
Non-polymers1,4975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3934
Polymers18,4951
Non-polymers8983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9926
Polymers18,4951
Non-polymers1,4975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0943
Polymers18,4951
Non-polymers5992
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3934
Polymers18,4951
Non-polymers8983
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9926
Polymers18,4951
Non-polymers1,4975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3934
Polymers18,4951
Non-polymers8983
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
N: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6925
Polymers18,4951
Non-polymers1,1974
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
O: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0943
Polymers18,4951
Non-polymers5992
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
16
P: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0943
Polymers18,4951
Non-polymers5992
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
17
Q: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3934
Polymers18,4951
Non-polymers8983
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
18
R: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6925
Polymers18,4951
Non-polymers1,1974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
19
S: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7942
Polymers18,4951
Non-polymers2991
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
20
T: Phenolic oxidative coupling protein


Theoretical massNumber of molelcules
Total (without water)18,4951
Polymers18,4951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
21
U: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9926
Polymers18,4951
Non-polymers1,4975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
22
V: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1904
Polymers18,4951
Non-polymers6953
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
23
W: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6925
Polymers18,4951
Non-polymers1,1974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
24
X: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4895
Polymers18,4951
Non-polymers9944
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
25
Y: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6925
Polymers18,4951
Non-polymers1,1974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
26
Z: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6315
Polymers18,4951
Non-polymers1,1364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
27
a: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7942
Polymers18,4951
Non-polymers2991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
28
b: Phenolic oxidative coupling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4895
Polymers18,4951
Non-polymers9944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.290, 146.290, 298.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE PROTEIN IS MONOMERIC IN SOLUTION, BUT FORMS DIMERS IN THE CRYSTAL STRUCTURE VIA ANTIPARALLEL INTERMOLECULAR BETA-SHEETS INVOLVING STRANDS BETA1. THE PAIRING SCHEME IS AB, CD, ..., YZ,...

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Components

#1: Protein ...
Phenolic oxidative coupling protein / Phenolic oxidative coupling protein Hyp-1


Mass: 18495.109 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypericum perforatum (plant) / Gene: hyp-1, HYP1.1 / Plasmid: pET151/D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8H1L1
#2: Chemical...
ChemComp-2AN / 8-ANILINO-1-NAPHTHALENE SULFONATE / 8-Anilinonaphthalene-1-sulfonic acid


Mass: 299.344 Da / Num. of mol.: 89 / Source method: obtained synthetically / Formula: C16H13NO3S
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES NUMBERED -5 TO 0 ARE FROM A CLONING ARTIFACT. RESIDUES 1-159 ARE FROM THE GENUINE PROTEIN ...RESIDUES NUMBERED -5 TO 0 ARE FROM A CLONING ARTIFACT. RESIDUES 1-159 ARE FROM THE GENUINE PROTEIN SEQUENCE. THE AMINO ACID SEQUENCE OF THE PRESENT PROTEIN DIFFERS FROM THE DEPOSITED SEQUENCE Q8H1L1 POSSIBLY BECAUSE OF GENETIC VARIABILITY

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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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES 0.1 M, tribasic sodium citrate 1.3 M, glycerol 10% , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2011 / Details: FOCUSING MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.251
11-K, -H, -L20.292
11-h,-k,l30.249
11K, H, -L40.209
ReflectionResolution: 2.43→50 Å / Num. obs: 61810 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 26.435
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2.64 / Num. unique all: 6043 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IE5
Resolution: 2.43→48.87 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: R-FREE / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. The reflection data set for refinement in monoclinic symmetry was obtained by expansion of a tetartohedrally twinned data set merged in tetragonal symmetry
RfactorNum. reflection% reflectionSelection details
Rfree0.27759 3077 1.3 %RANDOM
Rwork0.22278 ---
obs0.22353 232268 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.042 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-11.43 Å2
2---15.3 Å2-0 Å2
3---15.06 Å2
Refinement stepCycle: LAST / Resolution: 2.43→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35224 0 1914 35 37173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01938208
X-RAY DIFFRACTIONr_bond_other_d0.0010.0235737
X-RAY DIFFRACTIONr_angle_refined_deg2.1822.00551855
X-RAY DIFFRACTIONr_angle_other_deg3.648382416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.50754442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91924.9721619
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.043156308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5761584
X-RAY DIFFRACTIONr_chiral_restr0.1160.25475
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02142347
X-RAY DIFFRACTIONr_gen_planes_other0.0420.029027
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.141 16769 -
obs--96.96 %

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