[English] 日本語
Yorodumi
- PDB-3k7c: Crystal structure of Putative NTF2-like transpeptidase (NP_281412... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k7c
TitleCrystal structure of Putative NTF2-like transpeptidase (NP_281412.1) from CAMPYLOBACTER JEJUNI at 2.00 A resolution
ComponentsPutative NTF2-like transpeptidase
KeywordsPROTEIN BINDING / Putative NTF2-like transpeptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function
Function / homologyDomain of unknown function (DUF4878) / Domain of unknown function (DUF4878) / Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / DUF4878 domain-containing protein
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative NTF2-like transpeptidase (NP_281412.1) from CAMPYLOBACTER JEJUNI at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 / 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_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 ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative NTF2-like transpeptidase
B: Putative NTF2-like transpeptidase
C: Putative NTF2-like transpeptidase
D: Putative NTF2-like transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,90124
Polymers51,5854
Non-polymers2,31620
Water2,414134
1
A: Putative NTF2-like transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2945
Polymers12,8961
Non-polymers3984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative NTF2-like transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6657
Polymers12,8961
Non-polymers7696
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative NTF2-like transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6398
Polymers12,8961
Non-polymers7437
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative NTF2-like transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3034
Polymers12,8961
Non-polymers4063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.442, 89.807, 59.665
Angle α, β, γ (deg.)90.000, 110.500, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 6 - 113 / Label seq-ID: 7 - 114

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC STATE.

-
Components

#1: Protein
Putative NTF2-like transpeptidase


Mass: 12896.150 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: Cj0202c / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q0PBT7
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE THIS CONSTRUCT (1-113) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...SEQUENCE THIS CONSTRUCT (1-113) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 50.0000% PEG-200, 0.1M Citrate pH 5.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97908,0.97855
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 11, 2009 / 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
10.918371
20.979081
30.978551
ReflectionResolution: 2→28.571 Å / Num. obs: 31219 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.375 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.72
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.7171.2107485618192
2.07-2.150.5031.8114625978198.5
2.15-2.250.372.3120616287197.7
2.25-2.370.2892.9119416178198.4
2.37-2.520.2163.8118796161198.2
2.52-2.710.1515.4115715984197.8
2.71-2.990.0968.1122186293198.2
2.99-3.420.04914.7117336044197.9
3.42-4.30.02725.2116035969196.3
4.3-28.5710.0231.5119546129197.5

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→28.571 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 14.5 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.184
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. POLYETHYLENE GLYCOL (PEG AND PGE) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED INTO THE SOLVENT STRUCTURE. 5. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1576 5 %RANDOM
Rwork0.214 ---
obs0.216 31216 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.62 Å2 / Biso mean: 18.655 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20.98 Å2
2--0.08 Å20 Å2
3---2.03 Å2
Refinement stepCycle: LAST / Resolution: 2→28.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 141 134 3605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223550
X-RAY DIFFRACTIONr_bond_other_d0.0030.022467
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9874735
X-RAY DIFFRACTIONr_angle_other_deg1.21636100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.975447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5526.842152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17915670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2041510
X-RAY DIFFRACTIONr_chiral_restr0.0990.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023820
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02606
X-RAY DIFFRACTIONr_mcbond_it1.322185
X-RAY DIFFRACTIONr_mcbond_other0.242879
X-RAY DIFFRACTIONr_mcangle_it2.30843533
X-RAY DIFFRACTIONr_scbond_it3.03941365
X-RAY DIFFRACTIONr_scangle_it4.50261193
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A625MEDIUM POSITIONAL0.430.5
2B625MEDIUM POSITIONAL0.30.5
3C625MEDIUM POSITIONAL0.460.5
4D625MEDIUM POSITIONAL0.450.5
1A630LOOSE POSITIONAL0.555
2B630LOOSE POSITIONAL0.565
3C630LOOSE POSITIONAL0.655
4D630LOOSE POSITIONAL0.665
1A625MEDIUM THERMAL1.952
2B625MEDIUM THERMAL2.192
3C625MEDIUM THERMAL2.182
4D625MEDIUM THERMAL2.182
1A630LOOSE THERMAL2.4610
2B630LOOSE THERMAL2.2410
3C630LOOSE THERMAL2.7810
4D630LOOSE THERMAL2.7510
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 114 -
Rwork0.329 2166 -
all-2280 -
obs--98.66 %
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)
10.5182-0.7162-0.23676.5897-1.12150.35610.03340.2087-0.32650.1331-0.0933-0.0661-0.09770.04850.05990.14470.0341-0.01390.26-0.0450.288940.5449.23-15.732
28.3352-3.16242.02863.9199-1.23082.37240.0307-0.1153-0.0918-0.08940.0374-0.33610.0965-0.0721-0.06810.0780.00380.01540.21610.00110.108647.08619.632-12.873
39.64760.0897-0.50240.44790.94390.8786-0.18030.015-0.21-0.06710.0810.2767-0.19230.07070.09930.17370.0730.04890.26080.15320.403617.632.855-5.714
43.4109-2.74391.13788.3-2.93372.9705-0.2264-0.24830.31870.17170.44240.3947-0.0293-0.0732-0.2160.06110.0452-0.00080.26440.03340.161429.07135.939-7.885
56.62751.3454-2.07355.08031.17251.5708-0.0204-0.05930.43550.07980.0810.88740.03090.2305-0.06060.1621-0.079-0.03770.23650.07430.40542.14458.56212.061
63.04310.67960.14035.7961-1.1450.8823-0.14840.2363-0.0742-0.00260.20210.5287-0.00330.0999-0.05370.1161-0.06670.01160.23790.00160.150853.59658.37911.048
73.7665-0.7178-1.74247.21080.35310.89760.1348-0.00690.47240.2438-0.0616-0.4540.0010.1673-0.07320.208-0.0244-0.04580.21730.00870.320670.55482.74921.231
86.55591.0489-2.58983.6173-0.10582.4504-0.04950.27270.28280.29390.2019-0.3476-0.0888-0.2137-0.15240.13540.0117-0.07390.15990.02130.159870.29271.51917.204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 66
2X-RAY DIFFRACTION2A67 - 113
3X-RAY DIFFRACTION3B6 - 60
4X-RAY DIFFRACTION4B61 - 113
5X-RAY DIFFRACTION5C6 - 52
6X-RAY DIFFRACTION6C53 - 113
7X-RAY DIFFRACTION7D6 - 54
8X-RAY DIFFRACTION8D55 - 113

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more