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- PDB-2a2l: Crystal structure of Klebsiella pneumoniae protein ORFY, Pfam DUF336 -

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Basic information

Entry
Database: PDB / ID: 2a2l
TitleCrystal structure of Klebsiella pneumoniae protein ORFY, Pfam DUF336
Componentsunknown
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / UNKNOWN / PSI / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology: / Haem-degrading domain / Corrinoid adenosyltransferase PduO/GlcC-like / Corrinoid adenosyltransferase PduO/GlcC-like superfamily / Haem degrading protein HbpS-like / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsRamagopal, U. / Patskovsky, Y. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Klebsiella Pneumoniae Hypothetical Protein Orfy
Authors: Ramagopal, U. / Patskovsky, Y. / Almo, S.C.
History
DepositionJun 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: unknown
B: unknown
C: unknown
D: unknown


Theoretical massNumber of molelcules
Total (without water)61,4104
Polymers61,4104
Non-polymers00
Water10,052558
1
A: unknown
B: unknown
C: unknown
D: unknown

A: unknown
B: unknown
C: unknown
D: unknown


Theoretical massNumber of molelcules
Total (without water)122,8208
Polymers122,8208
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area26330 Å2
ΔGint-115 kcal/mol
Surface area38980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.490, 80.490, 207.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 4 - 146 / Label seq-ID: 3 - 145

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe assymetric unit contains tetramer (A,B,C,D), but the biological assembly is an octamer. The symmetry related second tetramer is generated be the two-fold axis -x+1, -y+1, z.

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Components

#1: Protein
unknown


Mass: 15352.450 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ORFY / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q48422
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.48 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% MPD, 0.1M HEPES, 0.2M Sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 87 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.989 / Wavelength: 0.989 Å
DetectorType: ADSC QUANTAM Q315 / Detector: CCD / Date: Mar 7, 2005 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 33912 / Num. obs: 32826 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.5 / Redundancy: 9.2 % / Rmerge(I) obs: 0.122 / Rsym value: 0.118 / Net I/σ(I): 6.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2765 / Rsym value: 0.222 / % possible all: 79.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data reduction
SOLVEphasing
RESOLVEmodel building
REFMAC5.2.0005refinement
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→103.69 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.812 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.333 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30788 1017 3.1 %RANDOM
Rwork0.23489 ---
all0.247 32826 --
obs0.23725 31792 92.35 %-
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: 27.415 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→103.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 0 558 4822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224304
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9515830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.485572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.82726.889180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.6515750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5521512
X-RAY DIFFRACTIONr_chiral_restr0.1170.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023176
X-RAY DIFFRACTIONr_nbd_refined0.190.32378
X-RAY DIFFRACTIONr_nbtor_refined0.3020.53069
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.5520
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.3127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.541
X-RAY DIFFRACTIONr_mcbond_it0.1310.052929
X-RAY DIFFRACTIONr_mcangle_it0.2180.054548
X-RAY DIFFRACTIONr_scbond_it7.58311533
X-RAY DIFFRACTIONr_scangle_it11.06431282
Refine LS restraints NCS

Ens-ID: 1 / Number: 1059 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.460.05
2Btight positional0.360.05
3Ctight positional0.380.05
4Dtight positional0.360.05
1Atight thermal3.41
2Btight thermal3.681
3Ctight thermal3.541
4Dtight thermal3.491
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 53 -
Rwork0.267 1972 -
obs-1972 79.26 %

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