PDB-8f0v: Lipocalin-like Milk protein-2 - E38A mutant

ID or keywords:

Entry

Database: PDB / ID: 8f0v

Title

Lipocalin-like Milk protein-2 - E38A mutant

Components

Milk protein

Keywords

LIPID BINDING PROTEIN / Lipocalin / Mutation / cockroach milk / Lili Mip.

Function / homology

Calycin / metal ion binding / Milk protein

Function and homology information

Biological species

Diploptera punctata (Pacific beetle cockroach)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.951 Å

Authors

Subramanian, R. / KanagaVijayan, D.

Funding support

1items

Citation

Journal: Plos One / Year: 2023
Title: Variability in phenylalanine side chain conformations facilitates broad substrate tolerance of fatty acid binding in cockroach milk proteins.
Authors: Santhakumari, P.R. / Dhanabalan, K. / Virani, S. / Hopf-Jannasch, A.S. / Benoit, J.B. / Chopra, G. / Subramanian, R.

History

Deposition	Nov 4, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 23, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8f0v.cif.gz	78.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8f0v.ent.gz	56.6 KB	Display	PDB format
PDBx/mmJSON format	8f0v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8f0v_validation.pdf.gz	448 KB	Display	wwPDB validaton report
Full document	8f0v_full_validation.pdf.gz	450 KB	Display
Data in XML	8f0v_validation.xml.gz	8.8 KB	Display
Data in CIF	8f0v_validation.cif.gz	10.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f0/8f0v ftp://data.pdbj.org/pub/pdb/validation_reports/f0/8f0v	HTTPS FTP

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Related structure data

Related structure data	8f0yC 7bkxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (1) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: Milk protein

hetero molecules

18.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	39.771, 52.337, 136.348
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	A-206- ZN

#1: Protein

Milk protein

Mass: 17958.211 Da / Num. of mol.: 1 / Mutation: E38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Diploptera punctata (Pacific beetle cockroach)
Production host:

Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q6SVB5

#2: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#3: Chemical

ChemComp-ZN / ZINC ION

Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.95 Å³/Da / Density % sol: 69 % / Description: diamond shaped crystals
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0 (0.002 M Zinc sulfate heptahydrate; 0.08 M HEPES pH 7.0; 25 % v/v Jeffamine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.07 Å
Detector	Type: RDI CMOS_8M / Detector: CMOS / Date: May 7, 2022 / Details: double crystal
Radiation	Monochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07 Å / Relative weight: 1
Reflection	Resolution: 2.95→38.18 Å / Num. obs: 6461 / % possible obs: 99.9 % / Redundancy: 6.6 % / B_iso Wilson estimate: 76 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.129 / R_pim(I) all: 0.054 / Net I/σ(I): 11.5
Reflection shell	Resolution: 2.95→3.13 Å / Redundancy: 6.9 % / R_merge(I) obs: 2 / Mean I/σ(I) obs: 1 / Num. unique obs: 1021 / CC_1/2: 0.58 / R_pim(I) all: 0.83 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7BKX

7bkx

Resolution: 2.951→38.18 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.907 / SU B: 22.75 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R: 0.806 / ESU R Free: 0.404
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2936	323	5.023 %
R_work	0.2345	6107	-
all	0.237	-	-
obs	-	6430	99.798 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 98.323 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.649 Å²	-0 Å²	0 Å²
2-	-	0.7 Å²	-0 Å²
3-	-	-	-7.349 Å²

Refinement step

Cycle: LAST / Resolution: 2.951→38.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1235	0	45	2	1282

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	1329
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.016	1107
X-RAY DIFFRACTION	r_angle_refined_deg	1.361	1.688	1816
X-RAY DIFFRACTION	r_angle_other_deg	0.432	1.566	2584
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.458	5	154
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	16.293	5	5
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.414	10	180
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.73	10	62
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	201
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1493
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	270
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	290
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.207	0.2	1169
X-RAY DIFFRACTION	r_nbtor_refined	0.19	0.2	639
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	692
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	38
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.001	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.122	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.093	0.2	8
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.033	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	7.836	10.196	619
X-RAY DIFFRACTION	r_mcbond_other	7.835	10.197	619
X-RAY DIFFRACTION	r_mcangle_it	12.306	15.255	772
X-RAY DIFFRACTION	r_mcangle_other	12.298	15.254	773
X-RAY DIFFRACTION	r_scbond_it	7.747	11.045	710
X-RAY DIFFRACTION	r_scbond_other	7.742	11.051	711
X-RAY DIFFRACTION	r_scangle_it	11.967	16.321	1044
X-RAY DIFFRACTION	r_scangle_other	11.962	16.325	1045
X-RAY DIFFRACTION	r_lrange_it	17.344	129.267	1460
X-RAY DIFFRACTION	r_lrange_other	17.345	129.303	1461

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.951-3.027	0.418	25	0.402	444	X-RAY DIFFRACTION	99.7872
3.027-3.109	0.531	21	0.392	430	X-RAY DIFFRACTION	100
3.109-3.199	0.251	17	0.379	409	X-RAY DIFFRACTION	100
3.199-3.296	0.433	30	0.331	413	X-RAY DIFFRACTION	100
3.296-3.404	0.289	19	0.316	372	X-RAY DIFFRACTION	100
3.404-3.522	0.338	17	0.271	394	X-RAY DIFFRACTION	100
3.522-3.654	0.205	23	0.242	367	X-RAY DIFFRACTION	100
3.654-3.802	0.247	27	0.243	334	X-RAY DIFFRACTION	100
3.802-3.969	0.311	20	0.209	354	X-RAY DIFFRACTION	100
3.969-4.16	0.473	13	0.183	323	X-RAY DIFFRACTION	99.7033
4.16-4.383	0.275	15	0.201	329	X-RAY DIFFRACTION	100
4.383-4.645	0.285	12	0.191	292	X-RAY DIFFRACTION	100
4.645-4.96	0.201	17	0.162	283	X-RAY DIFFRACTION	100
4.96-5.35	0.254	13	0.163	263	X-RAY DIFFRACTION	100
5.35-5.849	0.297	10	0.211	258	X-RAY DIFFRACTION	100
5.849-6.52	0.202	14	0.234	226	X-RAY DIFFRACTION	100
6.52-7.493	0.289	11	0.251	195	X-RAY DIFFRACTION	99.5169
7.493-9.09	0.366	8	0.2	176	X-RAY DIFFRACTION	100
9.09-12.506	0.28	7	0.221	148	X-RAY DIFFRACTION	99.359
12.506-38.18	0.333	4	0.31	97	X-RAY DIFFRACTION	95.283

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