HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 27-JUN-07 2JRM TITLE SOLUTION NMR STRUCTURE OF RIBOSOME MODULATION FACTOR VP1593 FROM TITLE 2 VIBRIO PARAHAEMOLYTICUS. NORTHEAST STRUCTURAL GENOMICS TARGET VPR55 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME MODULATION FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PARAHAEMOLYTICUS; SOURCE 3 ORGANISM_TAXID: 223926; SOURCE 4 STRAIN: RIMD 2210633; SOURCE 5 GENE: VP1593; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: VPR55-21.4; SOURCE 11 OTHER_DETAILS: THE PROTEIN IS A MONOMER BY GEL FILTRATION SOURCE 12 CHROMATOGRAPHY AND STATIC LIGHT SCATTERING. KEYWDS SOLUTION NMR STRUCTURE, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, UNKNOWN KEYWDS 3 FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.TANG,P.ROSSI,G.SWAPNA,H.WANG,M.JIANG,K.CUNNINGHAM,L.OWENS,L.MA, AUTHOR 2 R.XIAO,J.LIU,M.C.BARAN,T.B.ACTON,B.ROST,G.T.MONTELIONE,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 6 20-DEC-23 2JRM 1 REMARK REVDAT 5 04-DEC-19 2JRM 1 REMARK SEQADV SEQRES REVDAT 4 13-JUL-11 2JRM 1 VERSN REVDAT 3 24-FEB-09 2JRM 1 VERSN REVDAT 2 06-MAY-08 2JRM 1 SOURCE REVDAT 1 17-JUL-07 2JRM 0 JRNL AUTH Y.TANG,P.ROSSI,G.SWAPNA,H.WANG,M.JIANG,K.CUNNINGHAM,L.OWENS, JRNL AUTH 2 L.MA,R.XIAO,J.LIU,M.C.BARAN,T.B.ACTON,B.ROST,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF RIBOSOME MODULATION FACTOR VP1593 JRNL TITL 2 FROM VIBRIO PARAHAEMOLYTICUS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.11.2, CNS 1.1 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 865 COMFORMATIONALLY- REMARK 3 RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 154 DIHEDRAL ANGLE REMARK 3 CONSTRAINTS, AND 50 HYDROGEN BOND CONSTRAINTS (18.4 CONSTRAINTS REMARK 3 PER RESIDUE, 2.8 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR REMARK 3 RESIDUES 1 TO 60 BY PSVS 1.3) STRUCTURE DETERMINATION WAS REMARK 3 PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A REMARK 3 FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM REMARK 3 AUTOSTRUCTURE. THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE REMARK 3 FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY REMARK 3 MINIMIZATION IN EXPLICIT WATER (CNS). THE C-TERMINAL HIS TAG REMARK 3 RESDIUES OF THE PROTEIN (HHHHH) WERE INCLUDED IN ALL STRUCTURE REMARK 3 CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. REMARK 3 COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL REMARK 3 DETERMINED(S(PHI)+S(PSI)<1.8): 1-4, 54-60. THE STRUCTURE WAS REMARK 3 DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED REMARK 3 BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND THE SIDE CHAIN REMARK 3 ASSIGNMENTS WERE CO REMARK 3 PLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE, REMARK 3 HIHEDRAL ANGLE (HYPER) AND HYDROGEN BOND CONSTRAINTS WERE REMARK 3 DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENT REMARK 3 (EXCLUDING C-TERMINAL HHHHH): BACKBONE,99.66%, SIDE CHAIN, 92.20%, REMARK 3 AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, FINAL STRUCTURE REMARK 3 QUALITY FACTORS (FOR RESIDUE 1-60 PSVS 1.3), WHERE ORDERED REMARK 3 RESIDUES (S(PHI)+S(PSI)>1.8) COMPRISE: 5-54. (A) RMSD (ORDERED REMARK 3 RESIDUES): BB 0.5, HEAVY ATOM: 1.2 (B) RAMACHANDRAN STATISTICS FOR REMARK 3 ORDERED RESIDUES: MOST FAVORED, 83.6%, ADDITIONALLY ALLOWED: 13.8%, REMARK 3 GENEROUSLY ALLOWED : 0.2%, DISALLOWED,2.3%. (C) PROCHECK SCORES REMARK 3 FOR ORDERED RESIDUES (RAW/Z): PHI-PSI, -0.14/-0.24, ALL , -0.16/- REMARK 3 0.95. (D) MOLPROBITY CLASH SCORE (RAW/Z): 19.25/-1.78. (E) RPF REMARK 3 SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUE 1-60): RECALL, REMARK 3 0.962, PRECISION, 0.921, F-MEASURE, 0.941, DP-SCORE, 0.804. REMARK 4 REMARK 4 2JRM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000100202. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.1 MM [U-100% 13C; U-100% 15N] REMARK 210 VPR55, 20 MM MES, 100 MM NACL, 5 REMARK 210 MM CACL2, 10 MM DTT, 0.02 % NAN3, REMARK 210 95% H2O/5% D2O; 1.1 MM [U-5% REMARK 210 13C; U-100% 15N] VPR55, 20 MM REMARK 210 MES, 100 MM NACL, 5 MM CACL2, 10 REMARK 210 MM DTT, 0.02 % NAN3, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D REMARK 210 HNCO; 3D HNCACB; 3D CBCA(CO)NH; REMARK 210 3D HBHA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D CCH-TOCSY; 2D 1H- REMARK 210 13C HSQC_HIGH RESOLUTION REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, AUTOASSIGN 2.2.1, REMARK 210 SPARKY 3.110, AUTOSTRUCTURE REMARK 210 2.1.1, NMRPIPE, X-PLOR NIH REMARK 210 2.11.2, CNS 1.1, PSVS 1.3, REMARK 210 PDBSTAT 4.0, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 61 REMARK 465 HIS A 62 REMARK 465 HIS A 63 REMARK 465 HIS A 64 REMARK 465 HIS A 65 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 LYS A 2 -41.27 -152.76 REMARK 500 1 ARG A 3 47.33 -90.95 REMARK 500 1 ARG A 24 -64.52 64.93 REMARK 500 1 ALA A 28 40.28 -101.09 REMARK 500 1 PRO A 30 41.97 -97.41 REMARK 500 1 TYR A 31 -105.90 -119.36 REMARK 500 1 GLN A 33 -75.36 -101.62 REMARK 500 1 TYR A 39 -69.65 -96.95 REMARK 500 1 LEU A 55 49.35 -92.57 REMARK 500 2 ARG A 24 -43.26 73.40 REMARK 500 2 TYR A 31 -71.32 -70.18 REMARK 500 2 GLN A 33 -75.79 -98.17 REMARK 500 2 LEU A 55 67.86 62.13 REMARK 500 2 LYS A 57 86.07 77.75 REMARK 500 3 ARG A 3 39.19 -157.91 REMARK 500 3 ARG A 24 -63.24 60.68 REMARK 500 3 GLN A 33 -73.89 -101.08 REMARK 500 3 TYR A 39 -63.58 -95.29 REMARK 500 4 GLN A 4 12.42 -69.04 REMARK 500 4 ARG A 24 -68.51 61.08 REMARK 500 4 GLN A 33 -76.91 -102.51 REMARK 500 4 TYR A 39 -66.04 -94.81 REMARK 500 4 LEU A 55 -59.99 67.60 REMARK 500 4 TYR A 56 -60.72 -155.60 REMARK 500 4 LYS A 57 72.72 -159.41 REMARK 500 4 LEU A 58 -163.46 -100.45 REMARK 500 5 ARG A 24 -61.25 66.24 REMARK 500 5 TYR A 31 -68.33 -100.73 REMARK 500 5 GLN A 33 -76.01 -101.14 REMARK 500 5 LEU A 55 -62.15 -90.95 REMARK 500 5 TYR A 56 -64.58 69.14 REMARK 500 5 LYS A 57 22.29 161.74 REMARK 500 5 LEU A 58 -38.45 -142.82 REMARK 500 5 GLU A 59 88.72 66.15 REMARK 500 6 ARG A 24 -58.61 64.58 REMARK 500 6 PRO A 30 41.77 -92.33 REMARK 500 6 TYR A 31 -86.24 -113.14 REMARK 500 6 GLN A 33 -76.24 -99.57 REMARK 500 6 GLN A 52 -75.39 -87.11 REMARK 500 6 LEU A 55 88.74 61.23 REMARK 500 6 LYS A 57 79.42 73.80 REMARK 500 6 GLU A 59 101.89 -162.09 REMARK 500 7 ARG A 3 -62.93 -100.02 REMARK 500 7 ARG A 24 -55.48 69.03 REMARK 500 7 TYR A 31 -85.81 -99.40 REMARK 500 7 GLN A 33 -76.23 -101.13 REMARK 500 7 TYR A 39 -63.93 -99.98 REMARK 500 7 LEU A 55 61.41 -100.04 REMARK 500 7 LYS A 57 -56.53 -165.29 REMARK 500 7 GLU A 59 -157.40 -112.88 REMARK 500 REMARK 500 THIS ENTRY HAS 131 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NESG-VPR55 RELATED DB: TARGETDB REMARK 900 RELATED ID: 15339 RELATED DB: BMRB DBREF 2JRM A 1 57 UNP Q87PC4 Q87PC4_VIBPA 1 57 SEQADV 2JRM LEU A 58 UNP Q87PC4 CLONING ARTIFACT SEQADV 2JRM GLU A 59 UNP Q87PC4 CLONING ARTIFACT SEQADV 2JRM HIS A 60 UNP Q87PC4 CLONING ARTIFACT SEQADV 2JRM HIS A 61 UNP Q87PC4 CLONING ARTIFACT SEQADV 2JRM HIS A 62 UNP Q87PC4 CLONING ARTIFACT SEQADV 2JRM HIS A 63 UNP Q87PC4 CLONING ARTIFACT SEQADV 2JRM HIS A 64 UNP Q87PC4 CLONING ARTIFACT SEQADV 2JRM HIS A 65 UNP Q87PC4 CLONING ARTIFACT SEQRES 1 A 65 MET LYS ARG GLN LYS ARG ASP ARG LEU GLU ARG ALA GLN SEQRES 2 A 65 SER GLN GLY TYR LYS ALA GLY LEU ASN GLY ARG SER GLN SEQRES 3 A 65 GLU ALA CYS PRO TYR GLN GLN VAL ASP ALA ARG SER TYR SEQRES 4 A 65 TRP LEU GLY GLY TRP ARG ASP ALA ARG ASP GLU LYS GLN SEQRES 5 A 65 SER GLY LEU TYR LYS LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 ARG A 3 ASN A 22 1 20 HELIX 2 2 SER A 25 CYS A 29 5 5 HELIX 3 3 GLN A 33 GLY A 54 1 22 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1