PDB Short entry for 2JVD HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 18-SEP-07 2JVD TITLE SOLUTION NMR STRUCTURE OF THE FOLDED N-TERMINAL FRAGMENT OF UPF0291 TITLE 2 PROTEIN YNZC FROM BACILLUS SUBTILIS. NORTHEAST STRUCTURAL GENOMICS TITLE 3 TARGET SR384-1-46 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0291 PROTEIN YNZC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-46; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YNZC, BSU17880; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: SR384-1-46-21.1; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS SOLUTION NMR STRUCTURE, CONSTRUCT OPTIMIZATION, CYTOPLASM, STRUCTURAL KEYWDS 2 GENOMICS, UNKNOWN FUNCTION, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,S.SHARMA,Y.J.HUANG,L.ZHAO,L.A.OWENS,K.STOKES,M.JIANG, AUTHOR 2 R.XIAO,M.C.BARAN,G.V.T.SWAPNA,T.B.ACTON,G.T.MONTELIONE,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 6 08-MAY-24 2JVD 1 REMARK REVDAT 5 14-JUN-23 2JVD 1 REMARK REVDAT 4 19-FEB-20 2JVD 1 REMARK SEQADV REVDAT 3 24-FEB-09 2JVD 1 VERSN REVDAT 2 26-AUG-08 2JVD 1 JRNL REVDAT 1 02-OCT-07 2JVD 0 JRNL AUTH J.M.ARAMINI,S.SHARMA,Y.J.HUANG,G.V.SWAPNA,C.K.HO,K.SHETTY, JRNL AUTH 2 K.CUNNINGHAM,L.C.MA,L.ZHAO,L.A.OWENS,M.JIANG,R.XIAO,J.LIU, JRNL AUTH 3 M.C.BARAN,T.B.ACTON,B.ROST,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE SOS RESPONSE PROTEIN YNZC FROM JRNL TITL 2 BACILLUS SUBTILIS. JRNL REF PROTEINS V. 72 526 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18431750 JRNL DOI 10.1002/PROT.22064 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, CYANA 2.1 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 1022 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, 68 DIHEDRAL ANGLE CONSTRAINTS, AND 48 HYDROGEN BOND REMARK 3 CONSTRAINTS (25.9 CONSTRAINTS PER RESIDUE, 4.4 LONG RANGE REMARK 3 CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 48 BY PSVS REMARK 3 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING REMARK 3 CYANA 2.1. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET REMARK 3 FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ REMARK 3 ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19. REMARK 4 REMARK 4 2JVD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000100337. 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 : 1.36 MM [U-100% 13C; U-100% 15N] REMARK 210 SR384-1-46, 20 MM MES, 100 MM REMARK 210 SODIUM CHLORIDE, 10 MM DTT, 5 MM REMARK 210 CALCIUM CHLORIDE, 0.02 % SODIUM REMARK 210 AZIDE, 95% H2O/5% D2O; 1.1 MM [U- REMARK 210 5% 13C; U-100% 15N] SR384-1-46, REMARK 210 20 MM MES, 100 MM SODIUM REMARK 210 CHLORIDE, 10 MM DTT, 5 MM REMARK 210 CALCIUM CHLORIDE, 0.02 % SODIUM REMARK 210 AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HN(CA)CO; 3D HNCACB; REMARK 210 3D HN(COCA)CB; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-COSY; 3D CCH-TOCSY; 3D REMARK 210 SIMULTANEOUS CN-NOESY; 3D HNHA; REMARK 210 2D 1H-13C HSQC STEREOSPECIFIC REMARK 210 LEU/VAL METHYL REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AUTOASSIGN 2.4.0, CYANA 2.1, REMARK 210 NMRPIPE 2.3, AUTOSTRUCTURE 2.1.1, REMARK 210 PSVS 1.3, PDBSTAT 5.0, PROCHECK, REMARK 210 MOLPROBITY, SPARKY 3.110, VNMR REMARK 210 6.1C 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: THE PROTEIN IS MONOMERIC BY STATIC LIGHT SCATTERING. THE REMARK 210 STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR REMARK 210 SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING REMARK 210 AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED REMARK 210 MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING REMARK 210 CYANA 2.1. DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. REMARK 210 HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING BOTH REMARK 210 AUTOSTRUCTURE AND CYANA, AND WERE APPLIED ONLY IN THE FINAL REMARK 210 REFINEMENT STAGE (CNS) OF THE STRUCTURE DETERMINATION. REMARK 210 COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): REMARK 210 BACKBONE, 98.8%, SIDE CHAIN, 96.9%, AROMATICS, 100%, REMARK 210 STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100% REMARK 210 . FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 48, PSVS REMARK 210 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2- REMARK 210 38: (A) RMSD (ORDERED RESIDUES): BB, 0.4, HEAVY ATOM, 0.9. (B) REMARK 210 RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 98.6% REMARK 210 , ADDITIONALLY ALLOWED, 1.4%, GENEROUSLY ALLOWED, 0.0%, REMARK 210 DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/ REMARK 210 Z-): PHI-PSI, 0.53/2.40, ALL, 0.50/2.96. (D) MOLPROBITY CLASH REMARK 210 SCORE (RAW/Z-): 15.44/-1.12. (E) RPF SCORES FOR GOODNESS OF FIT REMARK 210 TO NOESY DATA (RESIDUES 1-48): RECALL, 0.988, PRECISION, 0.944, REMARK 210 F-MEASURE, 0.966, DP-SCORE, 0.822. (F) NUMBER OF CLOSE CONTACTS REMARK 210 PER 20 MODELS: NONE. THE C- TERMINAL HIS TAG RESIDUES OF THE REMARK 210 PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS REMARK 210 AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE REMARK 210 FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < REMARK 210 1.8]: 1,39-48. 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 49 REMARK 465 HIS A 50 REMARK 465 HIS A 51 REMARK 465 HIS A 52 REMARK 465 HIS A 53 REMARK 465 HIS A 54 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 39 99.65 -50.07 REMARK 500 3 LYS A 39 90.65 -60.63 REMARK 500 4 LYS A 39 90.44 -63.07 REMARK 500 4 LEU A 47 16.45 -164.26 REMARK 500 5 SER A 44 11.43 57.21 REMARK 500 5 LYS A 46 89.79 57.94 REMARK 500 7 LYS A 39 100.72 -58.02 REMARK 500 8 LYS A 39 91.85 -58.52 REMARK 500 9 SER A 43 -73.55 61.62 REMARK 500 9 SER A 44 28.79 40.78 REMARK 500 10 LEU A 38 -78.10 -81.27 REMARK 500 10 LEU A 47 -16.12 76.05 REMARK 500 11 LYS A 39 106.85 -56.53 REMARK 500 12 LYS A 39 95.78 -57.74 REMARK 500 13 LYS A 39 86.37 61.23 REMARK 500 13 ARG A 42 -56.97 72.06 REMARK 500 13 SER A 44 18.61 59.42 REMARK 500 13 LYS A 46 42.62 -84.88 REMARK 500 15 LYS A 39 96.29 -64.18 REMARK 500 15 ARG A 42 -4.87 -59.79 REMARK 500 16 LYS A 39 92.42 -56.39 REMARK 500 17 LYS A 39 91.22 -60.14 REMARK 500 17 LYS A 46 91.89 60.67 REMARK 500 17 LEU A 47 107.42 -173.70 REMARK 500 18 LYS A 39 99.51 -57.97 REMARK 500 18 SER A 43 -48.53 70.40 REMARK 500 18 SER A 44 97.95 -69.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SR384 RELATED DB: TARGETDB REMARK 900 RELATED ID: 15476 RELATED DB: BMRB REMARK 900 RELATED ID: 2HEP RELATED DB: PDB REMARK 900 SOLUTION NMR STRUCTURE OF FULL LENGTH PROTEIN YNZC DBREF 2JVD A 1 46 UNP O31818 YNZC_BACSU 1 46 SEQADV 2JVD LEU A 47 UNP O31818 EXPRESSION TAG SEQADV 2JVD GLU A 48 UNP O31818 EXPRESSION TAG SEQADV 2JVD HIS A 49 UNP O31818 EXPRESSION TAG SEQADV 2JVD HIS A 50 UNP O31818 EXPRESSION TAG SEQADV 2JVD HIS A 51 UNP O31818 EXPRESSION TAG SEQADV 2JVD HIS A 52 UNP O31818 EXPRESSION TAG SEQADV 2JVD HIS A 53 UNP O31818 EXPRESSION TAG SEQADV 2JVD HIS A 54 UNP O31818 EXPRESSION TAG SEQRES 1 A 54 MET ILE SER ASN ALA LYS ILE ALA ARG ILE ASN GLU LEU SEQRES 2 A 54 ALA ALA LYS ALA LYS ALA GLY VAL ILE THR GLU GLU GLU SEQRES 3 A 54 LYS ALA GLU GLN GLN LYS LEU ARG GLN GLU TYR LEU LYS SEQRES 4 A 54 GLY PHE ARG SER SER MET LYS LEU GLU HIS HIS HIS HIS SEQRES 5 A 54 HIS HIS HELIX 1 1 SER A 3 GLY A 20 1 18 HELIX 2 2 THR A 23 LYS A 39 1 17 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