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- PDB-3zg1: NI-BOUND FORM OF M123A MUTANT OF CUPRIAVIDUS METALLIDURANS CH34 CNRXS -

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Basic information

Entry
Database: PDB / ID: 3zg1
TitleNI-BOUND FORM OF M123A MUTANT OF CUPRIAVIDUS METALLIDURANS CH34 CNRXS
ComponentsNICKEL AND COBALT RESISTANCE PROTEIN CNRR
KeywordsMETAL BINDING PROTEIN / SENSOR PROTEIN / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


Heavy-metal resistance protein / Heavy-metal resistance / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1490 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Nickel and cobalt resistance protein CnrR
Similarity search - Component
Biological speciesCUPRIAVIDUS METALLIDURANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGirard, E. / Coves, J.
CitationJournal: Metallomics / Year: 2014
Title: Metal Sensing and Signal Transduction by Cnrx from Cupriavidus Metallidurans Ch34: Role of the Only Methionine Assessed by a Functional, Spectroscopic, and Theoretical Study
Authors: Trepreau, J. / Grosse, C. / Mouesca, J.-M. / Sarret, G. / Girard, E. / Petit-Haertlein, I. / Kuennemann, S. / Desbourdes, C. / De Rosny, E. / Maillard, A.P. / Nies, D.H. / Coves, J.
History
DepositionDec 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
B: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
C: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
D: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,56018
Polymers66,4034
Non-polymers1,15714
Water3,351186
1
C: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
D: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8529
Polymers33,2022
Non-polymers6507
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-40.8 kcal/mol
Surface area12510 Å2
MethodPISA
2
A: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
B: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7089
Polymers33,2022
Non-polymers5077
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-50.9 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.846, 79.125, 93.475
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
NICKEL AND COBALT RESISTANCE PROTEIN CNRR


Mass: 16600.791 Da / Num. of mol.: 4 / Fragment: METAL-SENSOR DOMAIN, RESIDUES 31-148 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CUPRIAVIDUS METALLIDURANS (bacteria) / Strain: CH34 / Plasmid: PET30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37975

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Non-polymers , 6 types, 200 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.26 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 16-20% PEG2000MME, 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2011 / Details: PT COATED MIRRORS IN A KIRKPATRICK-BAEZ GEOMETRY
RadiationMonochromator: HORIZONTALLY DIFFRACTING SI (111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.4
ReflectionResolution: 1.85→46.74 Å / Num. obs: 39483 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.5 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y3H
Resolution: 1.85→46.737 Å / σ(F): 1.89 / Phase error: 34.8 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2224 1987 5 %
Rwork0.1763 --
obs0.177 39447 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→46.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 62 186 3716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023713
X-RAY DIFFRACTIONf_angle_d0.5985014
X-RAY DIFFRACTIONf_dihedral_angle_d12.7251460
X-RAY DIFFRACTIONf_chiral_restr0.042544
X-RAY DIFFRACTIONf_plane_restr0.004684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8502-1.89650.33981420.31592623X-RAY DIFFRACTION93
1.8965-1.94770.32441340.2882667X-RAY DIFFRACTION95
1.9477-2.0050.32451510.26022665X-RAY DIFFRACTION94
2.005-2.06970.23761320.23732648X-RAY DIFFRACTION95
2.0697-2.14370.27351570.21512678X-RAY DIFFRACTION94
2.1437-2.22950.22411310.19822655X-RAY DIFFRACTION95
2.2295-2.3310.23581370.19582662X-RAY DIFFRACTION95
2.331-2.45390.25441530.18962708X-RAY DIFFRACTION94
2.4539-2.60760.26371400.18322649X-RAY DIFFRACTION95
2.6076-2.80880.22711350.17542684X-RAY DIFFRACTION95
2.8088-3.09130.22351450.17272697X-RAY DIFFRACTION95
3.0913-3.53840.20681440.15252721X-RAY DIFFRACTION95
3.5384-4.45670.17571410.13362658X-RAY DIFFRACTION94
4.4567-36.44070.19941350.14812746X-RAY DIFFRACTION95
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.8427-0.7786-0.59926.3164-6.11237.2187-0.21350.224-0.96480.15390.4520.53180.1984-1.25390.52690.2443-0.0047-0.06280.3719-0.10390.511412.521218.61977.1791
21.8928-1.3345-0.47153.356-1.40463.57020.0782-0.0263-0.27580.229-0.12420.2176-0.11670.05030.05170.1978-0.0213-0.00860.16680.00140.31838.954628.517213.2217
33.555-0.1622-0.98813.2945-1.9669.77880.1688-0.15650.1701-0.05760.02550.001-0.0418-0.0334-0.09550.220.05660.03910.19980.01120.28111.964136.8352-4.8412
41.71710.34950.77120.7546-0.28682.03740.13060.18570.4087-0.2126-0.1251-0.0653-0.2695-0.14150.06580.31540.09180.04270.18920.04550.292217.262640.8618-22.7562
52.28560.9609-1.42223.2418-4.08079.70840.1675-0.0343-0.03670.11250.0359-0.0462-0.3278-0.0564-0.25680.19140.01590.03140.1965-0.01130.244120.932835.8975-8.5809
62.1516-0.421-1.1621.5517-1.60242.8913-0.1291-0.2282-0.036-0.0603-0.0372-0.11360.11080.25010.16710.232-0.01250.01760.13250.0150.218619.269224.738113.077
73.8036-1.0665-3.31473.68621.41187.83950.0045-0.1234-0.5105-0.0339-0.19210.24840.44260.00450.15710.24830.0267-0.01110.14930.0020.337123.077714.99295.1294
85.79680.64530.93375.69141.28393.63790.293-0.3563-0.32860.2026-0.2145-0.37260.4947-0.35830.2380.2325-0.0421-0.00880.24990.06020.331913.302822.2687-25.3283
92.4254-0.65831.27462.89441.34378.4325-0.21680.0803-0.3715-0.3421-0.09120.10270.0039-0.04930.38460.32-0.00170.02670.12870.00820.360823.241119.93-33.5029
105.9684-0.3952.07148.12311.78462.0436-0.00870.21980.10570.16060.17840.06920.47680.3072-0.05380.3170.0730.01710.32560.02680.258528.470520.8187-17.2498
110.7528-0.18480.23492.2298-0.64513.78120.00620.05980.0285-0.1115-0.2034-0.02550.3950.22960.16560.25970.0352-0.00060.14040.00380.242930.498823.15033.0675
124.87560.02944.45971.24870.18924.3046-0.04710.3973-0.14170.11590.0719-0.2416-0.23230.47930.050.2508-0.01640.00040.11280.00440.294927.234229.717-8.5849
132.95881.68133.35221.29631.90729.0751-0.07810.36190.09440.05670.20790.3679-0.01770.6628-0.25430.19760.00540.01690.21220.04660.283222.217130.544-25.3851
142.12590.32890.44792.2533-0.21164.85420.0057-0.2692-0.21660.0441-0.01140.20690.185-0.34450.03570.15240.0222-0.00970.22650.01170.220810.812431.1411-28.8844
154.046-2.79661.92183.6245-4.17155.7198-0.0418-0.33640.54340.32030.1041.0527-0.76150.0145-0.16290.31260.00020.01230.2977-0.16020.6946-3.063145.362321.031
162.3075-0.35072.51454.1041-2.68835.0128-0.0596-0.30080.5529-0.25850.04890.1761-0.1756-0.352-0.02560.19030.0271-0.00960.1292-0.02360.3263-6.945837.27311.751
175.37480.00483.46010.2147-0.92516.2399-0.1025-0.13660.18310.0322-0.0119-0.48850.5498-0.79050.17070.2706-0.03050.0110.1625-0.04020.2686-4.079229.405827.2104
181.29150.6335-0.65581.916-0.10638.83270.09260.0890.04320.19490.0218-0.09990.0289-0.5281-0.16530.2583-0.0157-0.00360.20760.0190.2328-2.877326.041946.3901
191.0032-0.34790.46682.07770.91513.7297-0.1172-0.0185-0.0370.16750.2667-0.06230.16380.1482-0.19960.3323-0.029-0.02660.11180.03170.28935.993424.559348.4639
200.20450.0577-0.05920.3938-0.13360.799-0.0378-0.0015-0.12020.0731-0.00130.01350.1386-0.0028-0.11710.29610.0146-0.01080.02810.02590.36784.663831.049132.636
211.46660.18050.37832.5233-0.44952.4233-0.1779-0.18540.25930.2340.1061-0.1331-0.4185-0.2509-0.03430.27270.0309-0.0190.08640.00670.34375.177644.991216.411
223.0464-0.85531.29040.98-2.27846.6518-0.37130.22181.2399-0.27970.1992-1.2156-0.96230.01540.26340.4990.04420.05080.20330.09230.6386-1.992542.448.2495
236.16623.10734.95782.06023.31995.3786-0.3065-0.38941.93510.3917-0.16440.6683-0.2674-0.18030.7020.50010.12210.0830.4883-0.0440.674-2.064846.073259.9045
245.27730.6969-4.17812.1201-0.71488.6199-0.0227-0.29710.74550.12560.29690.2882-0.61270.4763-0.12660.3860.01140.04680.2633-0.02490.3288.216546.25258.1189
251.25470.11070.52760.991-1.07472.1813-0.0811-0.00770.0680.2892-0.2676-0.0097-1.34430.44380.11850.359-0.06230.00970.15020.00110.312613.631744.666636.2664
261.154-0.3783-1.00531.58490.26823.9777-0.15610.11960.22070.0481-0.1068-0.2233-0.01730.7410.28980.1902-0.03610.0110.16750.04810.277515.139138.503320.6673
270.67750.72380.56841.2279-0.68427.7031-0.1032-0.01770.158-0.0259-0.07750.0399-0.5301-0.32780.10650.235-0.01560.00710.09690.00390.29178.900935.710741.9946
281.5980.94241.67941.39720.67243.612-0.1205-0.02110.0609-0.15450.0373-0.0124-0.3645-0.37660.09160.21690.0280.03330.26860.0280.258-3.349134.919655.9683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 40:51)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 52:68)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 69:79)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 80:102)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 103:113)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 114:134)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 135:148)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 40:51)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 52:66)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 67:74)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 75:102)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 103:113)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 114:124)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 125:148)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 40:50)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 51:65)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 66:74)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 75:92)
19X-RAY DIFFRACTION19(CHAIN C AND RESID 93:103)
20X-RAY DIFFRACTION20(CHAIN C AND RESID 104:116)
21X-RAY DIFFRACTION21(CHAIN C AND RESID 117:148)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 39:45)
23X-RAY DIFFRACTION23(CHAIN D AND RESID 46:54)
24X-RAY DIFFRACTION24(CHAIN D AND RESID 55:67)
25X-RAY DIFFRACTION25(CHAIN D AND RESID 68:86)
26X-RAY DIFFRACTION26(CHAIN D AND RESID 87:104)
27X-RAY DIFFRACTION27(CHAIN D AND RESID 105:119)
28X-RAY DIFFRACTION28(CHAIN D AND RESID 120:148)

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