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- PDB-2ppv: CRYSTAL STRUCTURE OF a protein belonging to the UPF0052 (SE_0549)... -

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Basic information

Entry
Database: PDB / ID: 2ppv
TitleCRYSTAL STRUCTURE OF a protein belonging to the UPF0052 (SE_0549) FROM STAPHYLOCOCCUS EPIDERMIDIS ATCC 12228 AT 2.00 A RESOLUTION
ComponentsUncharacterized protein
KeywordsTRANSFERASE / PUTATIVE PHOSPHOTRANSFERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


regulation of cell shape / cytoplasm
Similarity search - Function
Gluconeogenesis factor / CofD-like domains / 2-phospho-L-lactate transferase CofD / CofD-like domain superfamily / 2-phospho-L-lactate transferase CofD / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Gluconeogenesis factor / Gluconeogenesis factor
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (NP_764104.1) from Staphylococcus epidermidis ATCC 12228 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: 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 1.3Oct 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 ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7852
Polymers36,6901
Non-polymers951
Water5,062281
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5714
Polymers73,3812
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area2420 Å2
ΔGint-35 kcal/mol
Surface area27450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)136.666, 136.814, 55.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Uncharacterized protein


Mass: 36690.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 12228 / Gene: NP_764104.1, SE_0549 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8CTE2, UniProt: A0A0H2VHQ6*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 3.56 Å3/Da / Density % sol: 65.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 0.2M Di-ammonium hydrogen phosphate, 25.0% PEG 3350, 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: 0.97931, 0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 2, 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
10.979311
20.918371
ReflectionResolution: 2→29.185 Å / Num. obs: 35353 / % possible obs: 98.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.46 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.054.10.870.81066226010.8799.7
2.05-2.114.10.6641.11037025410.66499.6
2.11-2.174.10.5281.41015824790.52899.6
2.17-2.244.10.4231.8999924310.42399.6
2.24-2.314.10.3581.9944722990.35899.6
2.31-2.394.10.2912.6926222470.29199.4
2.39-2.484.10.2562.9900221730.25699.2
2.48-2.584.10.1933.9859820830.19399
2.58-2.74.10.1544.8828120000.15499.1
2.7-2.834.10.1295.8797819230.12998.9
2.83-2.984.10.116.7755418250.1198.6
2.98-3.164.10.0947.4712117230.09498.5
3.16-3.384.10.088.5676916420.0898.4
3.38-3.654.10.0669.5617514890.06698.2
3.65-44.10.05610.9588114240.05697.8
4-4.474.10.04613.5513812490.04697.6
4.47-5.164.10.04613.1460111190.04697.2
5.16-6.324.10.0512.238529490.0597.4
6.32-8.9440.04513.229797490.04596.5
8.94-29.183.60.041614694070.0489.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→29.185 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.174 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.125
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RAMACHANDRAN OUTLIER A151 IS LOCATED IN POOR DENSITY. 5. UNMODELED DENSITY NEAR RESIDUES A13, A41, A126 AND A208 MAY BE PART OF THE ACTIVE SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1774 5 %RANDOM
Rwork0.171 ---
all0.173 ---
obs0.173 35338 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.661 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2→29.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 5 281 2707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222537
X-RAY DIFFRACTIONr_bond_other_d0.0010.022348
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9713473
X-RAY DIFFRACTIONr_angle_other_deg0.84735461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8175348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71325.472106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13815428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6051512
X-RAY DIFFRACTIONr_chiral_restr0.0910.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022873
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02459
X-RAY DIFFRACTIONr_nbd_refined0.2060.2490
X-RAY DIFFRACTIONr_nbd_other0.170.22358
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21298
X-RAY DIFFRACTIONr_nbtor_other0.0850.21559
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2192
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.215
X-RAY DIFFRACTIONr_mcbond_it2.3731700
X-RAY DIFFRACTIONr_mcbond_other0.5973674
X-RAY DIFFRACTIONr_mcangle_it3.56752685
X-RAY DIFFRACTIONr_scbond_it6.0428927
X-RAY DIFFRACTIONr_scangle_it8.80811776
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 129 -
Rwork0.238 2455 -
obs-2584 99.46 %
Refinement TLS params.Method: refined / Origin x: 48.562 Å / Origin y: 25.58 Å / Origin z: 27.409 Å
111213212223313233
T-0.1041 Å20.0173 Å20.021 Å2--0.0923 Å20.0087 Å2---0.0253 Å2
L1.1991 °2-0.6899 °2-0.3703 °2-1.2011 °20.3487 °2--0.9542 °2
S0.0211 Å °-0.0993 Å °0.06 Å °-0.0331 Å °0.0466 Å °-0.1544 Å °-0.0506 Å °-0.0015 Å °-0.0676 Å °
Refinement TLS groupSelection: ALL

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