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- PDB-3hl1: CRYSTAL STRUCTURE OF A FERRITIN LIKE PROTEIN (CC_0557) FROM CAULO... -

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Basic information

Entry
Database: PDB / ID: 3hl1
TitleCRYSTAL STRUCTURE OF A FERRITIN LIKE PROTEIN (CC_0557) FROM CAULOBACTER VIBRIOIDES AT 1.95 A RESOLUTION
ComponentsFerritin like protein
KeywordsMETAL BINDING PROTEIN / FERRITIN-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Helix Hairpins - #1530 / Iminophenyl-pyruvate dimer synthase / Ferritin-like / Helix Hairpins / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Unknown ligand / Iminophenyl-pyruvate dimer synthase domain-containing protein
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of ferritin like protein from Caulobacter crescentus CB15 (NP_419375.1) from Caulobacter crescentus at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 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 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin like protein
B: Ferritin like protein


Theoretical massNumber of molelcules
Total (without water)70,9614
Polymers70,9612
Non-polymers02
Water4,576254
1
A: Ferritin like protein


Theoretical massNumber of molelcules
Total (without water)35,4802
Polymers35,4801
Non-polymers01
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferritin like protein


Theoretical massNumber of molelcules
Total (without water)35,4802
Polymers35,4801
Non-polymers01
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.633, 44.017, 119.381
Angle α, β, γ (deg.)90.000, 96.170, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A4 - 178
2112B4 - 178
1212A182 - 292
2212B182 - 292
1312A299 - 316
2312B299 - 316
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Ferritin like protein


Mass: 35480.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: CB15 / Gene: CC_0557, NP_419375.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9AAP0
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
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.

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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: 2.01 Å3/Da / Density % sol: 38.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.93
Details: 17.5000% polyethylene glycol 6000, 0.1M citric acid pH 4.93, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97876,0.97828
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 22, 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
20.978761
30.978281
ReflectionResolution: 1.95→29.424 Å / Num. obs: 41306 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.88 % / Biso Wilson estimate: 31.69 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 12.61
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.95-2.020.5011.7153577676194.5
2.02-2.10.3372.5156767698196.4
2.1-2.20.2393.5168118208197.2
2.2-2.310.1664.9151457386197.3
2.31-2.460.1216.6167948131197.5
2.46-2.650.0829.4161287821197.8
2.65-2.910.05712.8159297729198
2.91-3.330.03519163587934197.9
3.33-4.190.02230.1160687801197
4.19-29.4240.01935.8159707752195.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
autoSHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→29.424 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 7.913 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.161
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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. THE B CHAIN IS SEVERELY DISORDERED. THE MODEL FOR B CHAIN WAS BUILT BASED ON THE CHAIN A WHERE DENSITY IS NOT DEFINITE. ADDITIONALLY, A291-297 HAS POOR DENSITY. 5. AN UNKNOWN LIGAND (UNL) IS MODELED FOR EACH MONOMER IN A SITE WHERE RESIDUES ARE HIGHLY CONSERVED.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2079 5 %RANDOM
Rwork0.185 ---
obs0.188 41295 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.06 Å2 / Biso mean: 39.863 Å2 / Biso min: 14.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å21.33 Å2
2--0.48 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 6 254 4684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224616
X-RAY DIFFRACTIONr_bond_other_d0.0020.023058
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9666331
X-RAY DIFFRACTIONr_angle_other_deg1.04437453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7035584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97823.775204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84115664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9071526
X-RAY DIFFRACTIONr_chiral_restr0.0890.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02947
X-RAY DIFFRACTIONr_nbd_refined0.2170.21047
X-RAY DIFFRACTIONr_nbd_other0.1790.23103
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22316
X-RAY DIFFRACTIONr_nbtor_other0.0850.22221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2224
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2960.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.212
X-RAY DIFFRACTIONr_mcbond_it2.00532991
X-RAY DIFFRACTIONr_mcbond_other0.90331155
X-RAY DIFFRACTIONr_mcangle_it2.96654672
X-RAY DIFFRACTIONr_scbond_it4.94181924
X-RAY DIFFRACTIONr_scangle_it6.567111652
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
1556TIGHT POSITIONAL0.050.05
1909MEDIUM POSITIONAL0.180.25
1556TIGHT THERMAL3.543
1909MEDIUM THERMAL4.058
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 149 -
Rwork0.242 2848 -
all-2997 -
obs--98.01 %
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)
11.46070.6398-0.29210.9563-0.51460.8664-0.02660.1783-0.0023-0.11650.04940.08650.0497-0.069-0.0228-0.08770.0324-0.0219-0.1236-0.0156-0.079932.72049.4326106.0087
21.6196-1.4065-0.8932.11941.1833.32430.1314-0.05520.14610.0706-0.0875-0.51320.09780.7003-0.04390.1615-0.14720.0560.1740.0224-0.031757.7182-2.632771.1475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 316
2X-RAY DIFFRACTION2B1 - 316

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