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- PDB-2p1a: Crystal structure of a putative metal-binding protein (bce_2162) ... -

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Basic information

Entry
Database: PDB / ID: 2p1a
TitleCrystal structure of a putative metal-binding protein (bce_2162) from bacillus cereus atcc 10987 at 2.10 A resolution
ComponentsHypothetical protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologydinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / DinB family protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_978475.1) from Bacillus cereus ATCC 10987 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Oct 9, 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: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)36,7182
Polymers36,7182
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-19 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.470, 77.820, 87.070
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
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSEILEILEAA1 - 312 - 32
21MSEMSEILEILEBB1 - 312 - 32
32SERSERLEULEUAA39 - 14040 - 141
42SERSERLEULEUBB39 - 14040 - 141

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Components

#1: Protein Hypothetical protein


Mass: 18359.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: NP_978475.1, BCE_2162 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q739H9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: NANODROP, 30.0% PEG 400, 0.1M CHES pH 9.5, 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: 0.91162, 0.97904, 0.97926
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 11, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979041
30.979261
ReflectionResolution: 2.1→29.566 Å / Num. obs: 18527 / % possible obs: 99.1 % / Biso Wilson estimate: 34.89 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 9.23
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allDiffraction-ID% possible all
2.1-2.190.3062.4559463603197.8
2.19-2.270.2433.0352183137199.3
2.27-2.380.2053.6561603685199.6
2.38-2.50.1684.4156073307199.5
2.5-2.660.1355.460173544199.4
2.66-2.860.0967.1757953369199.2
2.86-3.150.0699.5559883484199.7
3.15-3.60.04514.0859793434199.5
3.6-4.530.03419.959973478199.6
4.53-29.570.0322.660183430197.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.566 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.302 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.275 / ESU R Free: 0.217
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. RESIDUES 143-153 IN CHAIN A AND 150-153 IN CHAIN B ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 943 5.1 %RANDOM
Rwork0.221 ---
all0.223 ---
obs0.223 18482 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.995 Å2
Baniso -1Baniso -2Baniso -3
1--3.11 Å20 Å20 Å2
2---3.73 Å20 Å2
3---6.84 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 0 98 2470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212482
X-RAY DIFFRACTIONr_bond_other_d0.0030.021620
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9423373
X-RAY DIFFRACTIONr_angle_other_deg1.27433981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4165307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.74624.348115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24315445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.52157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022727
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02504
X-RAY DIFFRACTIONr_nbd_refined0.1720.2544
X-RAY DIFFRACTIONr_nbd_other0.1210.21533
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21171
X-RAY DIFFRACTIONr_nbtor_other0.0740.21161
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0740.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.219
X-RAY DIFFRACTIONr_mcbond_it1.89331589
X-RAY DIFFRACTIONr_mcbond_other0.3263597
X-RAY DIFFRACTIONr_mcangle_it2.72252400
X-RAY DIFFRACTIONr_scbond_it4.48481098
X-RAY DIFFRACTIONr_scangle_it6.02711965
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1745 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.555
LOOSE THERMAL3.0910
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 67 -
Rwork0.363 1211 -
obs-1278 94.18 %

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