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- PDB-3dza: Crystal structure of a putative membrane protein of unknown funct... -

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Basic information

Entry
Database: PDB / ID: 3dza
TitleCrystal structure of a putative membrane protein of unknown function (yfdx) from klebsiella pneumoniae subsp. at 1.65 A resolution
Componentsuncharacterized putative membrane protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


YfdX protein domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2140 / Uncharacterised protein family YfdX / YfdX protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Four Helix Bundle (Hemerythrin (Met), subunit A) / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / YfdX family protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative membrane protein of unknown function (YP_001337144.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized putative membrane protein
B: uncharacterized putative membrane protein
C: uncharacterized putative membrane protein
D: uncharacterized putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,64043
Polymers81,2014
Non-polymers2,43939
Water19,6361090
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23220 Å2
ΔGint-286 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.207, 79.016, 137.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 43 - 217 / Label seq-ID: 14 - 188

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
uncharacterized putative membrane protein


Mass: 20300.283 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
Gene: YP_001337144.1, yfdX, KPN78578_34530, KPN_03482 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6TE93
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1090 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 31-220 OF THE FULL LENGTH PROTEIN.

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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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 20.0000% PEG-3350, 0.2000M ZnAcetate, No Buffer pH 6.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97937,0.91837,0.97874
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 15, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
20.918371
30.978741
ReflectionResolution: 1.65→29.975 Å / Num. obs: 90273 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 13.584 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.693.90.6181.22566565870.61899.8
1.69-1.743.90.541.42512064080.5499.8
1.74-1.793.90.4591.72447662690.45999.8
1.79-1.843.90.38322381560710.38399.9
1.84-1.913.90.2992.62306058790.29999.9
1.91-1.973.90.2423.12249557410.24299.9
1.97-2.053.90.2013.82157854930.20199.9
2.05-2.133.90.1684.52094153300.16899.9
2.13-2.223.90.1425.22004751140.142100
2.22-2.333.90.1255.91924248990.125100
2.33-2.463.90.1096.71831646540.109100
2.46-2.613.90.10371745044400.103100
2.61-2.793.90.0927.81634441640.092100
2.79-3.013.90.0818.61523738910.081100
3.01-3.33.90.06610.11405935860.066100
3.3-3.693.90.05611.61276532710.056100
3.69-4.263.90.04912.91127029080.049100
4.26-5.223.80.04812.3953324910.048100
5.22-7.383.80.05211.9734219510.052100
7.38-29.983.50.04412.7396311260.04498.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→29.975 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.684 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.092
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ZINC, ACETATE (ACT) AND ETHYLENE GLYCEROL (EDO) MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. THE PRESENCE OF HEAVY ATOMS AT ZINC POSITIONS IS SUPPORTED BY ANOMALOUS DIFFERENCE MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 4525 5 %RANDOM
Rwork0.152 ---
obs0.154 90207 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.232 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2---0.59 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5314 0 126 1090 6530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225758
X-RAY DIFFRACTIONr_bond_other_d0.0010.023895
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.987796
X-RAY DIFFRACTIONr_angle_other_deg0.90939682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6815802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47826.583240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.116151076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5991521
X-RAY DIFFRACTIONr_chiral_restr0.0850.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02994
X-RAY DIFFRACTIONr_nbd_refined0.2180.21293
X-RAY DIFFRACTIONr_nbd_other0.1830.24068
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22815
X-RAY DIFFRACTIONr_nbtor_other0.0880.22960
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2879
X-RAY DIFFRACTIONr_metal_ion_refined0.1880.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.234
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0150.21
X-RAY DIFFRACTIONr_mcbond_it1.9934019
X-RAY DIFFRACTIONr_mcbond_other0.6931489
X-RAY DIFFRACTIONr_mcangle_it2.3955905
X-RAY DIFFRACTIONr_scbond_it4.88982240
X-RAY DIFFRACTIONr_scangle_it6.363111841
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1005MEDIUM POSITIONAL0.130.5
2B1005MEDIUM POSITIONAL0.130.5
3C1005MEDIUM POSITIONAL0.220.5
4D1005MEDIUM POSITIONAL0.160.5
1A973LOOSE POSITIONAL0.515
2B973LOOSE POSITIONAL0.445
3C973LOOSE POSITIONAL0.55
4D973LOOSE POSITIONAL0.555
1A1005MEDIUM THERMAL0.872
2B1005MEDIUM THERMAL1.082
3C1005MEDIUM THERMAL1.142
4D1005MEDIUM THERMAL0.912
1A973LOOSE THERMAL1.7610
2B973LOOSE THERMAL1.8410
3C973LOOSE THERMAL1.9210
4D973LOOSE THERMAL1.6510
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 315 -
Rwork0.215 6269 -
all-6584 -
obs--99.65 %

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