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- PDB-2gx8: The Crystal Structure of Bacillus cereus protein related to NIF3 -

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Basic information

Entry
Database: PDB / ID: 2gx8
TitleThe Crystal Structure of Bacillus cereus protein related to NIF3
ComponentsNIF3-related protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NIF3 related protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


metal ion binding / cytoplasm
Similarity search - Function
DUF34/NIF3, bacteria / DUF34/NIF3 / Duf34/NIF3 (NGG1p interacting factor 3) / DUF34/NIF3 superfamily / Alpha-Beta Plaits - #120 / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / GTP cyclohydrolase 1 type 2 homolog
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsMinasov, G. / Brunzelle, J.S. / Shuvalova, L. / Vorontsov, I.I. / Collart, F.R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2007
Title: The 2.2 A resolution crystal structure of Bacillus cereus Nif3-family protein YqfO reveals a conserved dimetal-binding motif and a regulatory domain
Authors: Godsey, M.H. / Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Vorontsov, I.I. / Collart, F.R. / Anderson, W.F.
History
DepositionMay 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_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_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_ref_seq_dif.details / _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: NIF3-related protein
B: NIF3-related protein
C: NIF3-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,65815
Polymers130,9523
Non-polymers1,70612
Water11,097616
1
A: NIF3-related protein
B: NIF3-related protein
C: NIF3-related protein
hetero molecules

A: NIF3-related protein
B: NIF3-related protein
C: NIF3-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,31730
Polymers261,9056
Non-polymers3,41224
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area33360 Å2
ΔGint-533 kcal/mol
Surface area88720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.036, 95.036, 260.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

DetailsThe biologiacl assembly is a hexamer generated from the trimer in the asymmetric unit by the operation: x-y, -y, -z+1/3

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Components

#1: Protein NIF3-related protein


Mass: 43650.789 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: AAP11199 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: GenBank: 29897924, UniProt: Q818H0*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 0.25M NaCl, 25%w/v PEG1000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.94642 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 30, 2005 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94642 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 68204 / Num. obs: 68204 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 5.48 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 34.89
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 3.14 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.69 / Num. unique all: 10144 / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata scaling
SHARPphasing
RESOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→28.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.938 / SU B: 17.905 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26123 3421 5 %RANDOM
Rwork0.19572 ---
obs0.199 65026 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.759 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20.78 Å20 Å2
2--1.56 Å20 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8366 0 89 616 9071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228615
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9711656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.35451080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23325.606371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.418151519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9851521
X-RAY DIFFRACTIONr_chiral_restr0.1190.21327
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026342
X-RAY DIFFRACTIONr_nbd_refined0.20.33867
X-RAY DIFFRACTIONr_nbtor_refined0.3150.55870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.5858
X-RAY DIFFRACTIONr_metal_ion_refined0.020.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.3184
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.573
X-RAY DIFFRACTIONr_mcbond_it1.0961.55518
X-RAY DIFFRACTIONr_mcangle_it1.77228662
X-RAY DIFFRACTIONr_scbond_it3.09233416
X-RAY DIFFRACTIONr_scangle_it4.5954.52994
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 217 -
Rwork0.36 4097 -
obs--84.65 %
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)
13.2732-1.19440.86056.49591.59252.9372-0.05920.0343-0.1228-0.24830.2471-0.1314-0.03030.1124-0.188-0.4304-0.16520.11390.1395-0.1702-0.128933.96829.094320.5061
23.72890.72672.44733.60931.277410.92080.1023-0.00590.1709-0.41350.00840.07880.2380.2961-0.1107-0.23870.0775-0.0008-0.34450.0112-0.247716.4207-25.01243.8448
32.82810.6939-2.00174.59670.95288.053-0.0201-0.083-0.29660.00920.2052-0.31420.42240.1682-0.1851-0.46510.0051-0.06820.1264-0.23110.061545.5785-12.694836.3002
42.3201-0.87113.47242.6788-0.96148.91160.12440.3989-0.2991-0.60230.4179-0.4232-0.10240.8505-0.5423-0.3423-0.10530.21390.288-0.2710.074145.00052.595618.7716
51.32340.4925-0.29982.87940.99716.10980.11-0.1785-0.1346-0.1275-0.1055-0.1596-0.0030.158-0.0045-0.48650.0375-0.0249-0.0790.0052-0.2698-19.1463-1.284130.1646
63.90160.08580.630712.16223.14635.0514-0.0554-0.4855-0.31550.4745-0.13142.28520.6433-1.24760.1869-0.1194-0.12590.04780.15160.01820.2950.2339-32.18512.4961
74.78610.93040.33336.91443.01363.5408-0.08920.2761-0.077-0.65330.1659-0.5461-0.2474-0.0329-0.0767-0.29870.03060.1057-0.168-0.0483-0.2277-1.284713.117211.5378
84.21494.54081.22897.51941.26042.2954-0.14860.2778-0.0101-0.2930.28620.19760.0311-0.2516-0.1375-0.40220.0968-0.0362-0.0051-0.0334-0.3368-20.70153.680218.2354
95.15922.72390.95845.2532.31254.4772-0.2190.6081-0.2777-0.0740.3226-0.31180.35660.407-0.1036-0.28820.1479-0.00980.0062-0.1564-0.122919.6425-29.308456.7382
105.6852-0.515-2.82575.5680.55329.07620.2043-0.7725-0.66480.425-0.2291-0.11611.09580.38570.0247-0.00890.0489-0.1077-0.13010.1286-0.160418.91-38.314118.0347
112.6975-0.6267-4.57340.75460.58078.1348-0.17590.4908-0.3233-0.0511-0.18440.18820.7228-0.41120.3602-0.2005-0.1651-0.02590.0134-0.1283-0.1229-3.5145-31.914944.711
123.976-1.27580.53162.03240.05322.20080.0940.2533-0.41820.07580.0437-0.18820.66730.1176-0.1378-0.1317-0.0419-0.0296-0.1461-0.1231-0.11683.5222-31.9856.9422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 11028 - 134
2X-RAY DIFFRACTION2AA131 - 244155 - 268
3X-RAY DIFFRACTION3AA111 - 130135 - 154
4X-RAY DIFFRACTION3AA245 - 333269 - 357
5X-RAY DIFFRACTION4AA334 - 373358 - 397
6X-RAY DIFFRACTION5BB4 - 11028 - 134
7X-RAY DIFFRACTION6BB131 - 243155 - 267
8X-RAY DIFFRACTION7BB111 - 130135 - 154
9X-RAY DIFFRACTION7BB244 - 330268 - 354
10X-RAY DIFFRACTION8BB331 - 373355 - 397
11X-RAY DIFFRACTION9CC4 - 11028 - 134
12X-RAY DIFFRACTION10CC131 - 222155 - 246
13X-RAY DIFFRACTION11CC111 - 130135 - 154
14X-RAY DIFFRACTION11CC223 - 309247 - 333
15X-RAY DIFFRACTION12CC310 - 373334 - 397

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