HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 21-JUN-06 2HEP
TITLE SOLUTION NMR STRUCTURE OF THE UPF0291 PROTEIN YNZC FROM BACILLUS
TITLE 2 SUBTILIS. NORTHEAST STRUCTURAL GENOMICS TARGET SR384.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: UPF0291 PROTEIN YNZC;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS;
SOURCE 3 ORGANISM_TAXID: 1423;
SOURCE 4 GENE: YNZC;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21, SR384-21.4
KEYWDS SR384, AUTOSTRUCTURE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, PSI-
KEYWDS 2 1, PROTEIN STRUCTURE INITIATIVE, NESG, STRUCTURAL GENOMICS, UNKNOWN
KEYWDS 3 FUNCTION
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR J.M.ARAMINI,G.V.T.SWAPNA,C.K.HO,K.SHETTY,K.CUNNINGHAM,L.-C.MA,R.XIAO,
AUTHOR 2 J.LIU,M.BARAN,T.B.ACTON,B.ROST,G.T.MONTELIONE,NORTHEAST STRUCTURAL
AUTHOR 3 GENOMICS CONSORTIUM (NESG)
REVDAT 4 09-MAR-22 2HEP 1 REMARK SEQADV
REVDAT 3 24-FEB-09 2HEP 1 VERSN
REVDAT 2 10-JUN-08 2HEP 1 JRNL
REVDAT 1 15-AUG-06 2HEP 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 : VNMR 6.1C, AUTOSTRUCTURE 2.1.1, XPLOR-NIH 2.11.2
REMARK 3 AUTHORS : VARIAN (VNMR), HUANG & MONTELIONE (AUTOSTRUCTURE),
REMARK 3 CLORE ET AL (XPLOR-NIH)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 403 CONFORMATIONALLY
REMARK 3 RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 67 DIHEDRAL ANGLE
REMARK 3 CONSTRAINTS, 42 HYDROGEN BOND CONSTRAINTS, AND 29 J(HN-HALPHA)
REMARK 3 COUPLING CONSTANTS (12.5 CONSTRAINTS PER RESIDUE; 1.1 LONG RANGE
REMARK 3 CONSTRAINTS PER RESIDUE; COMPUTED FOR RESIDUES 1 TO 42 BY PSVS 1.2)
REMARK 3 .
REMARK 3 STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING
REMARK 3 AUTOSTRUCTURE (XPLOR-NIH). A FINAL XPLOR CALCULATION USING THE
REMARK 3 FINAL CONSTRAINTS DERIVED FROM AUTOSTRUCTURE WAS PERFORMED TO
REMARK 3 YIELD THE FINAL STRUCTURES. THE UNSTRUCTURED C-TERMINAL HALF OF
REMARK 3 THE MOLECULE WAS INCLUDED IN ALL STRUCTURAL CALCULATIONS BUT HAS
REMARK 3 BEEN OMITTED FROM THIS DEPOSITION. HETERONUCLEAR 15N,1H NOE
REMARK 3 EXPERIMENTS CORROBORATE THE PRESENCE OF SIGNIFICANT DISORDER IN
REMARK 3 THE C-TERMINAL HALF OF THE PROTEIN (RESIDUES 43 TO C-TERMINUS).
REMARK 4
REMARK 4 2HEP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-06.
REMARK 100 THE DEPOSITION ID IS D_1000038262.
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 MM NACL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.12MM U-13C,15N SR384, 20MM
REMARK 210 MES, 100MM NACL, 5 MM CACL2,
REMARK 210 10MM DTT, 0.02% NAN3, PH 6.5, 5%
REMARK 210 D2O/95% H2O; 1.12MM 5%-13C,U-15N
REMARK 210 SR384, 20MM MES, 100MM NACL, 5
REMARK 210 MM CACL2, 10MM DTT, 0.02% NAN3,
REMARK 210 PH 6.5, 5% D2O/95% H2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY; HNHA; 3D GFT-
REMARK 210 CBCACACONHN, GFT-HNNCACBCA, GFT-
REMARK 210 HABCABCONHN; 3D HCCH-TOCSY,
REMARK 210 CCCONH TOCSY, HCCH-COSY; HIGH
REMARK 210 RESOLUTION 2D CH-HQSC (FOR
REMARK 210 STEREOSPECIFIC ASSIGNMENT OF VAL/
REMARK 210 LEU METHYLS); 3D HNCO, HNCACO;
REMARK 210 2D 15N1H-HETERONUCLEAR NOE
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 3.5PL6, AUTOASSIGN
REMARK 210 2.2.1, SPARKY 3.110, AGNUS 2.0,
REMARK 210 PDBSTAT 4.01, PSVS 1.2
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 LOWEST
REMARK 210 CONFORMATIONAL ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK:
REMARK 210 THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR
REMARK 210 SPECTROSCOPY. AUTOASSIGN WAS USED TO OBTAIN AUTOMATIC BACKBONE
REMARK 210 ASSIGNMENTS FROM GFT PEAK LISTS. SIDE CHAIN ASSIGNMENTS WERE
REMARK 210 COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENT, AS WELL AS
REMARK 210 DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING
REMARK 210 AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING
REMARK 210 HYPER. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL
REMARK 210 LEHHHHHH TAG):
REMARK 210 BACKBONE: 91.9%; SIDE CHAIN: 78.3%; AROMATICS, 100%:
REMARK 210 STEREOSPECIFIC METHYL, 87.5%.
REMARK 210 FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 42 ONLY; PSVS
REMARK 210 1.2), WHERE ORDERED RESIDUES [S(PHI)+ S(PSI) > 1.8] COMPRISE 5-20
REMARK 210 AND 23-40:
REMARK 210 (A) RMSD (ORDERED RESIDUES): BB, 0.9; HEAVY ATOM, 1.5. (B)
REMARK 210 RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 96.4%,
REMARK 210 ADDITIONALLY ALLOWED, 3.6%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED,
REMARK 210 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI,
REMARK 210 0.11/0.75; ALL, -0.12/-0.71. (D) MOLPROBITY CLASH SCORE (RAW/Z-):
REMARK 210 14.69/-1.00. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA
REMARK 210 (ALL RESIDUES): RECALL, 0.952, PRECISION, 0.839, F-MEASURE, 0.892,
REMARK 210 DP-SCORE, 0.628
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 SER A 43
REMARK 465 SER A 44
REMARK 465 MET A 45
REMARK 465 LYS A 46
REMARK 465 ASN A 47
REMARK 465 THR A 48
REMARK 465 LEU A 49
REMARK 465 LYS A 50
REMARK 465 SER A 51
REMARK 465 VAL A 52
REMARK 465 LYS A 53
REMARK 465 ILE A 54
REMARK 465 ILE A 55
REMARK 465 ASP A 56
REMARK 465 PRO A 57
REMARK 465 GLU A 58
REMARK 465 GLY A 59
REMARK 465 ASN A 60
REMARK 465 ASP A 61
REMARK 465 VAL A 62
REMARK 465 THR A 63
REMARK 465 PRO A 64
REMARK 465 GLU A 65
REMARK 465 LYS A 66
REMARK 465 LEU A 67
REMARK 465 LYS A 68
REMARK 465 ARG A 69
REMARK 465 GLU A 70
REMARK 465 GLN A 71
REMARK 465 ARG A 72
REMARK 465 ASN A 73
REMARK 465 ASN A 74
REMARK 465 LYS A 75
REMARK 465 LEU A 76
REMARK 465 HIS A 77
REMARK 465 LEU A 78
REMARK 465 GLU A 79
REMARK 465 HIS A 80
REMARK 465 HIS A 81
REMARK 465 HIS A 82
REMARK 465 HIS A 83
REMARK 465 HIS A 84
REMARK 465 HIS A 85
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 O TYR A 37 H PHE A 41 1.55
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 SER A 3 19.85 -170.27
REMARK 500 1 ASN A 4 -156.70 -77.92
REMARK 500 1 VAL A 21 -38.78 -156.37
REMARK 500 1 ILE A 22 132.21 69.80
REMARK 500 1 PHE A 41 -106.85 19.89
REMARK 500 2 ILE A 2 -70.38 -108.71
REMARK 500 2 SER A 3 -113.97 44.74
REMARK 500 2 ASN A 4 -159.56 43.12
REMARK 500 2 VAL A 21 -63.89 -152.11
REMARK 500 2 ILE A 22 146.36 69.05
REMARK 500 3 ASN A 4 -68.42 -142.45
REMARK 500 3 ARG A 9 -75.91 -60.10
REMARK 500 3 VAL A 21 99.17 67.05
REMARK 500 3 PHE A 41 -77.02 -66.42
REMARK 500 4 SER A 3 -45.13 73.40
REMARK 500 4 VAL A 21 -36.79 -156.61
REMARK 500 4 ILE A 22 97.45 41.41
REMARK 500 4 PHE A 41 93.87 -172.63
REMARK 500 5 SER A 3 14.51 -156.80
REMARK 500 5 ARG A 9 -74.30 -60.17
REMARK 500 5 VAL A 21 94.59 67.41
REMARK 500 6 SER A 3 -138.36 59.77
REMARK 500 6 ASN A 4 -104.42 57.06
REMARK 500 6 VAL A 21 100.67 -177.20
REMARK 500 6 PHE A 41 -87.70 -64.20
REMARK 500 7 SER A 3 89.10 47.02
REMARK 500 7 ASN A 4 -155.26 -165.78
REMARK 500 7 VAL A 21 -45.75 -159.67
REMARK 500 7 ILE A 22 122.63 67.99
REMARK 500 8 ILE A 2 -13.63 -162.02
REMARK 500 8 ASN A 4 -79.01 -153.04
REMARK 500 8 VAL A 21 -65.07 74.61
REMARK 500 8 ILE A 22 138.59 129.34
REMARK 500 9 SER A 3 65.68 -173.19
REMARK 500 9 ASN A 4 -113.80 -171.85
REMARK 500 9 ARG A 9 -73.81 -61.13
REMARK 500 9 ASN A 11 -70.08 -59.01
REMARK 500 9 VAL A 21 99.45 74.39
REMARK 500 9 PHE A 41 98.88 -64.32
REMARK 500 10 SER A 3 80.06 41.05
REMARK 500 10 ASN A 4 -142.81 -154.91
REMARK 500 10 VAL A 21 76.26 49.32
REMARK 500 10 ILE A 22 -130.46 -87.85
REMARK 500 10 GLU A 29 -70.37 -59.42
REMARK 500 10 PHE A 41 98.17 -172.93
REMARK 500 11 ILE A 2 94.39 55.48
REMARK 500 11 ASN A 4 -154.34 -138.32
REMARK 500 11 VAL A 21 99.65 -172.75
REMARK 500 11 PHE A 41 -161.01 90.23
REMARK 500 12 ASN A 4 -118.91 -173.55
REMARK 500
REMARK 500 THIS ENTRY HAS 91 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: SR384 RELATED DB: TARGETDB
DBREF 2HEP A 1 77 UNP O31818 YNZC_BACSU 1 77
SEQADV 2HEP LEU A 78 UNP O31818 CLONING ARTIFACT
SEQADV 2HEP GLU A 79 UNP O31818 CLONING ARTIFACT
SEQADV 2HEP HIS A 80 UNP O31818 EXPRESSION TAG
SEQADV 2HEP HIS A 81 UNP O31818 EXPRESSION TAG
SEQADV 2HEP HIS A 82 UNP O31818 EXPRESSION TAG
SEQADV 2HEP HIS A 83 UNP O31818 EXPRESSION TAG
SEQADV 2HEP HIS A 84 UNP O31818 EXPRESSION TAG
SEQADV 2HEP HIS A 85 UNP O31818 EXPRESSION TAG
SEQRES 1 A 85 MET ILE SER ASN ALA LYS ILE ALA ARG ILE ASN GLU LEU
SEQRES 2 A 85 ALA ALA LYS ALA LYS ALA GLY VAL ILE THR GLU GLU GLU
SEQRES 3 A 85 LYS ALA GLU GLN GLN LYS LEU ARG GLN GLU TYR LEU LYS
SEQRES 4 A 85 GLY PHE ARG SER SER MET LYS ASN THR LEU LYS SER VAL
SEQRES 5 A 85 LYS ILE ILE ASP PRO GLU GLY ASN ASP VAL THR PRO GLU
SEQRES 6 A 85 LYS LEU LYS ARG GLU GLN ARG ASN ASN LYS LEU HIS LEU
SEQRES 7 A 85 GLU HIS HIS HIS HIS HIS HIS
HELIX 1 1 ASN A 4 VAL A 21 1 18
HELIX 2 2 THR A 23 PHE A 41 1 19
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
(ATOM LINES ARE NOT SHOWN.)
END
