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- PDB-3go0: Crystal structure of D-enantiomer of human alpha-defensin 1 (D-HNP1) -

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Basic information

Entry
Database: PDB / ID: 3go0
TitleCrystal structure of D-enantiomer of human alpha-defensin 1 (D-HNP1)
ComponentsNeutrophil defensin 1
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide / D-enantiomer of human alpha defensin 1 / D-enantiomer of human neutrophil peptide 1 / D-HNP1
Function / homologypolypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsPazgier, M. / Lu, W.-Y.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Through the looking glass, mechanistic insights from enantiomeric human defensins.
Authors: Wei, G. / de Leeuw, E. / Pazgier, M. / Yuan, W. / Zou, G. / Wang, J. / Ericksen, B. / Lu, W.Y. / Lehrer, R.I. / Lu, W.
History
DepositionMar 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 7, 2018Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Sep 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_ncs_dom_lim
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_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neutrophil defensin 1
B: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0115
Polymers6,9042
Non-polymers1063
Water1,11762
1
A: Neutrophil defensin 1
B: Neutrophil defensin 1
hetero molecules

A: Neutrophil defensin 1
B: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,02110
Polymers13,8084
Non-polymers2136
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area3120 Å2
ΔGint-81 kcal/mol
Surface area7620 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-35 kcal/mol
Surface area4200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.277, 31.098, 40.281
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DAL / Beg label comp-ID: DAL / End auth comp-ID: DCY / End label comp-ID: DCY / Refine code: 6 / Auth seq-ID: 1 - 30 / Label seq-ID: 1 - 30

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Polypeptide(D) Neutrophil defensin 1 / HNP-1 / HP-1 / HP1 / Defensin / alpha 1 / HP 1-56 / Neutrophil defensin 2 / HNP-2 / HP-2 / HP2


Mass: 3452.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: D-enantiomer / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE DATABASE REFERENCE FOR THE L-FORM SEQUENCE IS UNP ENTRY P59665 AND INCLUDES RESIDUES ...THE SEQUENCE DATABASE REFERENCE FOR THE L-FORM SEQUENCE IS UNP ENTRY P59665 AND INCLUDES RESIDUES 65-94. THE SEQUENCE TRANSLATES TO L-PROTEIN AS FOLLOWS ACYCRIPACIAGERRYGTCIYQGRLWAFCC.

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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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 sodium citrate tribasic dehydrate, 0.1 M HEPES, pH 7.5, 20% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 12, 2008 / Details: confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.56→40.281 Å / Num. all: 8495 / Num. obs: 8404 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.078 / Rsym value: 0.112
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 9.7 / Num. unique all: 339 / Rsym value: 0.204 / % possible all: 84.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0070refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GNY

3gny


Resolution: 1.56→12 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.191 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.091 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES, RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.199 390 4.7 %RANDOM
Rwork0.187 ---
obs0.187 7988 99.01 %-
all-8378 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.72 Å2 / Biso mean: 16.886 Å2 / Biso min: 9.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--1.41 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.56→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms476 0 3 62 541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02484
X-RAY DIFFRACTIONr_angle_refined_deg1.7822.469644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.279554
X-RAY DIFFRACTIONr_chiral_restr0.1110.264
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02354
X-RAY DIFFRACTIONr_mcbond_it0.6051.5292
X-RAY DIFFRACTIONr_mcangle_it1.0452452
X-RAY DIFFRACTIONr_scbond_it1.4443192
X-RAY DIFFRACTIONr_scangle_it2.3344.5192
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 238 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.545
LOOSE THERMAL2.0610
LS refinement shellResolution: 1.56→1.603 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 36 -
Rwork0.22 559 -
all-595 -
obs--99.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76030.3749-0.24392.8341-0.07291.41010.0404-0.02750.0755-0.0151-0.0173-0.0094-0.12610.0623-0.02310.0974-0.0036-0.00620.1052-0.00250.1227-14.5948.3882-14.0998
22.6096-0.7679-0.00692.44550.58632.9536-0.031-0.09730.07490.18730.0309-0.11410.04040.24250.00010.10150.0006-0.01170.11890.00390.1096-11.0741-1.2174-5.8351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2B1 - 30

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