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Yorodumi- PDB-1vrc: Complex of enzyme IIAmannose and the histidine-containing phospho... -
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-Basic information
Entry | Database: PDB / ID: 1vrc | |||||||||
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Title | Complex of enzyme IIAmannose and the histidine-containing phosphocarrier protein HPr from escherichia coli nmr, restrained regularized mean structure | |||||||||
Components |
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Keywords | TRANSFERASE / PHOSPHOTRANSFERASE / KINASE / SUGAR TRANSPORT / COMPLEX (TRANSFERASE-PHOSPHOCARRIER) | |||||||||
Function / homology | Function and homology information protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / glucose import across plasma membrane / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex ...protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / glucose import across plasma membrane / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / enzyme inhibitor activity / enzyme activator activity / enzyme regulator activity / kinase activity / phosphorylation / protein homodimerization activity / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | SOLUTION NMR / CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS | |||||||||
Authors | Clore, G.M. / Williams, D.C. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Solution NMR structure of the 48-kDa IIAMannose-HPr complex of the Escherichia coli mannose phosphotransferase system. Authors: Williams, D.C. / Cai, M. / Suh, J.Y. / Peterkofsky, A. / Clore, G.M. | |||||||||
History |
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Remark 7 | IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL ... IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. IT IS IMPORTANT TO NOTE THAT THE VALUES GIVEN FOR THE BACKBONE ATOMS AND NON-INTERFACIAL SIDECHAINS PROVIDE ONLY A MEASURE OF THE PRECISION WITH WHICH THE RELATIVE ORIENTATION OF THE TWO PROTEINS HAVE BEEN DETERMINED AND DOES NOT TAKE INTO ACCOUNT THE ERRORS IN THE X-RAY COORDINATES OF HPR AND IIAMAN. RESIDUE NUMBERING: IIAMAN: 1-136 (THE N-TERMINAL METHIONINE IS CLEAVED AND RESIDUES 131-136 WERE DISORDERED. RESIDUES 134-136 ARE CLONING ARTIFACTS; SEE REMARKS IN THE 1PDO CRYSTAL STRUCTURE.) HPR: 201-285 (CORRESPONDING TO RESIDUES 1-85). PHOSPHATES: RESIDUES 401 AND 402. TWO SETS OF COORDINATES ARE GIVEN: MODEL 1: RESTRAINED REGULARIZED MEAN COORDINATES FOR THE MODEL OF THE ASSOCIATIVE PHOSPHORYL TRANSITION STATE HPR-IIAMTL COMPLEX. EXPERIMENTAL RESTRAINTS ARE IDENTICAL TO THOSE USED FOR MODEL 2, BUT COVALENT GEOMETRY RESTRAINTS ARE INCLUDED RELATING TO THE PENTACOORDINATE PHOSPHORYL GROUP IN A TRIGONAL BIPYRAMIDAL GEOMETRY. THE STRUCTURE IS DERIVED FROM MODEL 2 BY RESTRAINED REGULARIZATION IN WHICH ONLY THE ACTIVE SITE HISTIDINES, THE BACKBONE IMMIEDIATELY ADJACENT (ONE RESIDUE ON EITHER SIDE) TO THE ACTIVE SITE HISTIDINES, AND THE INTERFACIAL SIDECHAINS ARE ALLOWED TO MOVE. THE N-P BOND LENGTHS ARE RESTRAINED TO 2 A. IIAMAN-HPR COMPLEX RMS DEVIATIONS FROM NOE DISTANCE RESTRAINTS: 0.009 A RMS DEVIATIONS FROM SIDECHAIN TORSION ANGLE RESTRAINTS: 0.0 DEG. DIPOLAR COUPLING R-FACTORS (CLORE AND GARRETT (1999) J. AM. CHEM. SOC. 121, 9008-9012): IIAMAN HPr NH 11.6 18.5/12.4 MODEL 2: RESTRAINED REGULARIZED MEAN COORDINATES OF THE UNPHOSPHORYLATED IIAMAN-HPR COMPLEX SOLVED ON THE BASIS OF 58x2 INTERMOLECULAR INTERPROTON DISTANCE DISTANCE RESTRAINTS BETWEEN THE TWO MOLECULES OF HPR AND THE IIAMAN DIMER, 47x2 INTRA AND 16x2 INTER-SUBUNIT IIAMAN DISTANCE RESTRAINTS RELATING ONLY TO INTERFACIAL SIDECHAINS, 39x2 INTRAMOLECULAR HPR cwDISTANCE RESTRAINTS RELATING ONLY TO INTERFACIAL SIDECHAINS, 29x2 INTERFACIAL SIDECHAIN TORSION ANGLE RESTRAINTS, 92X2 RESIDUAL DIPOLAR COUPLINGS FOR IIAMAN AND 66X2 RESIDUAL DIPOLAR COUPLINGS FOR HPR. WAS USED FOR THE DIPOLAR COUPLINGS (CLORE AND GARRETT (1999) J. AM. CHEM. SOC. 121, 9008-9012). NOTE THE NH DIPOLAR COUPLINGS FOR FULLY BOUND HPR (I.E. BOTH BIDNING SITES ON IIAMAN FULLY SATURATED) ARE BACKCALCULATED FROM THE DIPOLAR COUPLINGS MEASURED FOR A SAMPLE WITH A THREE-FOLD MOLAR EXCESS OF HPR OVER IIAMAN BINDING SITES AND A SAMPLE OF FREE HPR. THE FIRST VALUE OF THE R-FACTOR USES DIPOLAR COUPLINGS FOR THE FULLY BOUND STATE BACK-CALCULATED USING THE MEASURED VALUES OF THE DIPOLAR OUPLINGS FOR FREE HPR; WHILE THE SECOND NUMBER USES THE CALCULATED VALUES OF THE DIPOLAR COUPLINGS FOR FREE HPR DERIVED FROM THE MEASURED VALUES AND THE CRYSTAL STRUCTURE OF FREE HPR USING SINGULAR VALUE DECOMPOSITION. NOTE A SINGLE ALIGNMENT TENSOR IS USED. THE DIPOLAR COUPLING R-FACTOR OBTAINED BY SINGULAR VALUE DECOMPOSITION AGAINST THE CRYSTAL STRUCTURES OF IIAMAN AND HPR INDIVIDUAL ARE THE SAME AS THOSE OBTAINED FOR THE COMPLEX AS A WHOLE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vrc.cif.gz | 270.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vrc.ent.gz | 226.2 KB | Display | PDB format |
PDBx/mmJSON format | 1vrc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/1vrc ftp://data.pdbj.org/pub/pdb/validation_reports/vr/1vrc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14755.821 Da / Num. of mol.: 2 / Fragment: EIIA DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: manX, gptB, ptsL / Production host: Escherichia coli (E. coli) References: UniProt: P69797, protein-Npi-phosphohistidine-sugar phosphotransferase #2: Protein | Mass: 9129.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ptsH, hpr / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA04 #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | Ionic strength: 40 mM SODIUM PHOSPHATE / pH: 6.5 / Temperature: 308.00 K |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS / Software ordinal: 1 Details: THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302). THE TARGET FUNCTIONS COMPRISES TERMS FOR NOE RESTRAINTS, ...Details: THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302). THE TARGET FUNCTIONS COMPRISES TERMS FOR NOE RESTRAINTS, SIDECHAIN TORSION ANGLE RESTRAINTS, RESIDUAL DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON.133, 216-221(1998)), A RADIUS OF GYRATION TERM (KUSZEWSKI ET AL.(1999), A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129- 136), AND A TORSION ANGLE CONFORMATIONAL DATABASE POTENTIAL OF MEAN FORCE (CLORE AND KUSZEWSKI 2002) J.AM.CHEM.SOC 124, 2866-2867). THE STARTING COORDINATE COME FROM THE X-RAY STRUCTURES (WITH PROTONS ADDED) OF E. COLI HPR (1POH, JIA ET AL. (1993) J.BIOL.CHEM. 268, 22940-22501, RESOLUTION 2.0 A); AND IIAMAN (1PDO, NUNN ET AL. (1996) J.MOL.BI J.MOL.BIOL. 259, 502-511; RESOLUTION 1.7A). THE BACKBONE COORDINATES AND NON-INTERFACIAL SIDECHAINS ARE TREATED AS RIGID BODIES THROUGHOUT WITH THE IIAMAN DIMER HELD FIXED, THE TWO HPR MOLECULES ALLOWED TO ROTATE AND TRANSLATE, AND THE AXIS OF THE SINGLE DIPOLAR COUPLING ALIGNMENT TENSOR FREE TO ROTATE. THE INTERFACIAL SIDECHAINS ARE GIVEN FULL TORSIONAL DEGREES OF FREEDOM. | ||||||||||||
NMR ensemble | Conformer selection criteria: REGULARIZED MEAN STRUCTURES / Conformers calculated total number: 100 / Conformers submitted total number: 2 |