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- PDB-2nlh: Human beta-defensin-1 (Mutant GLN24ALA) -

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Basic information

Entry
Database: PDB / ID: 2nlh
TitleHuman beta-defensin-1 (Mutant GLN24ALA)
ComponentsBeta-defensin 1Beta defensin
KeywordsANTIMICROBIAL PROTEIN / antimicrobial / chemotactic / defensin / mutant
Function / homology
Function and homology information


positive regulation of flagellated sperm motility involved in capacitation / microvesicle / CCR6 chemokine receptor binding / Beta defensins / Defensins / : / sperm midpiece / cAMP-mediated signaling / innate immune response in mucosa / response to bacterium ...positive regulation of flagellated sperm motility involved in capacitation / microvesicle / CCR6 chemokine receptor binding / Beta defensins / Defensins / : / sperm midpiece / cAMP-mediated signaling / innate immune response in mucosa / response to bacterium / Golgi lumen / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / immune response / G protein-coupled receptor signaling pathway / innate immune response / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding
Similarity search - Function
Beta defensin type / Beta defensin
Similarity search - Domain/homology
ACETATE ION / Beta-defensin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLubkowski, J. / Pazgier, M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Studies of the Biological Properties of Human beta-Defensin 1.
Authors: Pazgier, M. / Prahl, A. / Hoover, D.M. / Lubkowski, J.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-defensin 1
B: Beta-defensin 1
C: Beta-defensin 1
D: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,17011
Polymers15,5344
Non-polymers6357
Water3,531196
1
A: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1724
Polymers3,8841
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0763
Polymers3,8841
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0393
Polymers3,8841
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-defensin 1


Theoretical massNumber of molelcules
Total (without water)3,8841
Polymers3,8841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Beta-defensin 1

B: Beta-defensin 1
hetero molecules

A: Beta-defensin 1
C: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,17011
Polymers15,5344
Non-polymers6357
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_556-x,y+1/2,-z+11
crystal symmetry operation2_646-x+1,y-1/2,-z+11
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-117 kcal/mol
Surface area8810 Å2
MethodPISA
6
B: Beta-defensin 1
hetero molecules

D: Beta-defensin 1


Theoretical massNumber of molelcules
Total (without water)7,9594
Polymers7,7672
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area1270 Å2
ΔGint-46 kcal/mol
Surface area4830 Å2
MethodPISA
7
A: Beta-defensin 1
C: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2107
Polymers7,7672
Non-polymers4435
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-50 kcal/mol
Surface area4920 Å2
MethodPISA
8
C: Beta-defensin 1
hetero molecules

B: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1146
Polymers7,7672
Non-polymers3474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area950 Å2
ΔGint-46 kcal/mol
Surface area5290 Å2
MethodPISA
9
A: Beta-defensin 1
hetero molecules

D: Beta-defensin 1


Theoretical massNumber of molelcules
Total (without water)8,0555
Polymers7,7672
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area880 Å2
ΔGint-45 kcal/mol
Surface area5240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.590, 26.770, 59.600
Angle α, β, γ (deg.)90.00, 102.60, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is a monomer

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Components

#1: Protein/peptide
Beta-defensin 1 / Beta defensin / BD-1 / Defensin / beta 1 / hBD-1


Mass: 3883.547 Da / Num. of mol.: 4 / Fragment: human beta-defensins 1, residues 33-68 / Mutation: Q24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEFB1, BD1, HBD1 / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysE / References: UniProt: P60022
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: PEG 4000, AMMONIUM SULFATE, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 15, 2005 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 12097 / Num. obs: 12097 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.066 / Χ2: 0.947 / Net I/σ(I): 27
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1204 / Χ2: 0.698 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.401data extraction
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IJV

1ijv


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.454 / SU ML: 0.109 / SU R Cruickshank DPI: 0.159 / Cross valid method: THROUGHOUT / ESU R Free: 0.154 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 577 4.8 %RANDOM
Rwork0.185 ---
all0.188 12083 --
obs0.188 12083 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.692 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å2-0.03 Å2
2--0.29 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 34 197 1307
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01911350.022
X-RAY DIFFRACTIONr_angle_refined_deg1.66215301.985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2331405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.523622.222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89118915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.142415
X-RAY DIFFRACTIONr_chiral_restr0.1131550.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0088120.02
X-RAY DIFFRACTIONr_nbd_refined0.2394940.2
X-RAY DIFFRACTIONr_nbtor_refined0.37750.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1911430.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2211100.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.154260.2
X-RAY DIFFRACTIONr_mcbond_it1.2657381.5
X-RAY DIFFRACTIONr_mcangle_it1.97311292
X-RAY DIFFRACTIONr_scbond_it2.7424643
X-RAY DIFFRACTIONr_scangle_it3.9064014.5
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 36 -
Rwork0.294 830 -
obs-866 98.19 %
Refinement TLS params.Origin x: 7.9202 Å / Origin y: 7.7736 Å / Origin z: 20.3556 Å
111213212223313233
T-0.1193 Å20.0262 Å2-0.0097 Å2--0.0634 Å20.0084 Å2---0.0753 Å2
L0.0945 °20.1007 °20.0713 °2-0.3136 °20.0454 °2--0.0584 °2
S0.0109 Å °-0.0682 Å °-0.0477 Å °-0.0161 Å °-0.0512 Å °-0.0218 Å °-0.0061 Å °-0.0768 Å °0.0403 Å °
Refinement TLS groupSelection: ALL

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