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- PDB-3ord: Structural Evidence for Stabilization of Inhibitor Binding by a P... -

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Basic information

Entry
Database: PDB / ID: 3ord
TitleStructural Evidence for Stabilization of Inhibitor Binding by a Protein Cavity in the Dehaloperoxidase-Hemoglobin from Amphitrite ornata
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / globin / peroxidase
Function / homology
Function and homology information


oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / XENON / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
Authorsde Serrano, V.S. / Franzen, S.
CitationJournal: Biopolymers / Year: 2012
Title: Structural evidence for stabilization of inhibitor binding by a protein cavity in the dehaloperoxidase-hemoglobin from Amphitrite ornata.
Authors: de Serrano, V. / Franzen, S.
History
DepositionSep 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Sep 6, 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_site
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_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: Dehaloperoxidase A
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,04710
Polymers31,0972
Non-polymers1,9508
Water2,072115
1
A: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6206
Polymers15,5491
Non-polymers1,0715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4284
Polymers15,5491
Non-polymers8793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.674, 67.805, 68.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer

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Components

#1: Protein Dehaloperoxidase A


Mass: 15548.597 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Gene: dhp A / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9NAV8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Xe
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.2 M ammonium sulfate, 32% PEG 4000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Jul 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.22→48.121 Å / Num. all: 13324 / Num. obs: 12423 / % possible obs: 93.24 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 16.8
Reflection shellResolution: 2.22→2.278 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 3.3 / Num. unique all: 974 / % possible all: 83.61

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2qfk

2qfk


Resolution: 2.22→30.5 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.871 / SU B: 8.192 / SU ML: 0.209 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2889 635 4.9 %RANDOM
Rwork0.21203 ---
obs0.21563 12423 93.24 %-
all-13323 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.841 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20 Å2
2---1.15 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.22→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 100 115 2397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222701
X-RAY DIFFRACTIONr_angle_refined_deg1.3752.0553730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4645369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33824.138145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.2615507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4841524
X-RAY DIFFRACTIONr_chiral_restr0.0970.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022162
X-RAY DIFFRACTIONr_mcbond_it0.6011.51531
X-RAY DIFFRACTIONr_mcangle_it1.07822503
X-RAY DIFFRACTIONr_scbond_it1.81731170
X-RAY DIFFRACTIONr_scangle_it2.8334.51178
LS refinement shellResolution: 2.22→2.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 38 -
Rwork0.261 814 -
obs-814 83.61 %

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