HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 21-JUN-06 2HEQ
TITLE NMR STRUCTURE OF BACILLUS SUBTILIS PROTEIN YORP, NORTHEAST STRUCTURAL
TITLE 2 GENOMICS TARGET SR399.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: YORP PROTEIN;
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: YORP;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(LAMDA DE3) PMGK;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21
KEYWDS SH3-LIKE, BSU2030, YORP, NESG, STRUCTURAL GENOMICS, PSI-2, PROTEIN
KEYWDS 2 STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM,
KEYWDS 3 UNKNOWN FUNCTION
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR T.A.RAMELOT,J.R.CORT,D.WANG,H.JANJUA,K.CUNNINGHAM,L.-C.MA,R.XIAO,
AUTHOR 2 J.LIU,M.BARAN,G.V.T.SWAPNA,T.B.ACTON,B.ROST,G.M.MONTELIONE,
AUTHOR 3 M.A.KENNEDY,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)
REVDAT 3 09-MAR-22 2HEQ 1 REMARK SEQADV
REVDAT 2 24-FEB-09 2HEQ 1 VERSN
REVDAT 1 15-AUG-06 2HEQ 0
JRNL AUTH T.A.RAMELOT,J.R.CORT,R.XIAO,G.V.T.SWAPNA,T.B.ACTON,
JRNL AUTH 2 G.T.MONTELIONE,M.A.KENNEDY
JRNL TITL NMR STRUCTURE OF BACILLUS SUBTILIS PROTEIN YORP, NORTHEAST
JRNL TITL 2 STRUCTURAL GENOMICS TARGET SR399.
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SPARKY 3.1, X-PLOR-NIH 2.10, CNS 1.1
REMARK 3 AUTHORS : T.D. GODDARD, D.G. KNELLER (SPARKY), C.D.
REMARK 3 SCHWIETERS, J.J. KUSZEWSKI, N. TJANDRA, G.M. CLORE
REMARK 3 (X-PLOR-NIH), A. BRUNGER, G.L. WARREN (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 590 RESTRAINTS. 507 ARE NOE-
REMARK 3 DERIVED; SEQUENTIAL [(I-J)=1] = 101; MEDIUM RANGE [1<(I-J)<5] = 87;
REMARK 3 LONG RANGE [(I-J)>=5] = 315; HYDROGEN BOND RESTRAINTS = 30 (2 PER
REMARK 3 H-BOND); NUMBER OF NOE RESTRAINTS PER RESIDUE = 6.9 (RESIDES 3-76);
REMARK 3 DIHEDRAL-ANGLE RESTRAINTS = 53 (26 PHI, 27 PSI); TOTAL NUMBER OF
REMARK 3 RESTRAINTS PER RESIDUE = 8.0 (RESIDES 3-76); NUMBER OF LONG RANGE
REMARK 3 RESTRAINTS PER RESIDUE = 4.3; NUMBER OF STRUCTURES COMPUTED = 20;
REMARK 3 NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.1
REMARK 3 ANG = 0; AVERAGE RMS DISTANCE VIOLATION / CONSTRAINT = 0.004
REMARK 3 ANGSTROMS.; MAXIMUM DISTANCE VIOLATION 0.05. AVERAGE DIHEDRAL
REMARK 3 ANGLE VIOLATIONS: >10 DEG = 0; MAX DIHEDRAL ANGLE VIOLATION = 0.45;
REMARK 3 AVERAGE RMS ANGLE VIOLATION / CONSTRAINT = 0.14 DEG. RMSD VALUES:
REMARK 3 BACKBONE ATOMS (N,C,C', RESIDUES 11-20,33-68) = 0.4 ANG; ALL HEAVY
REMARK 3 ATOMS = 0.9 ANG;
REMARK 3 PROCHECK (RESIDUES 11-20,33-68): MOST FAVORED REGIONS = 95%;
REMARK 3 ADDITIONAL ALLOWED REGIONS = 5%; GENEROUSLY ALLOWED REGIONS = 0%;
REMARK 3 DISALLOWED REGIONS = 1%.
REMARK 3
REMARK 3 6 NON-NATIVE N-TERMINAL RESIDUES (MAGDPL) AND 8 C-TERMINAL
REMARK 3 RESDIUES, INLUDING THE HIS TAG, (LEHHHHHH) WERE INCLUDED IN THE
REMARK 3 STRUCTURE CALCULATION.
REMARK 4
REMARK 4 2HEQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-06.
REMARK 100 THE DEPOSITION ID IS D_1000038263.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 5.5
REMARK 210 IONIC STRENGTH : 100MM NACL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.1MM YORP, U-15N, 13C; 20 MM
REMARK 210 NH4OAC, 100MM NACL, 10MM DTT,
REMARK 210 5MM CACL2, 0.02% NAN3, 95% H2O,
REMARK 210 5% D2O; 1MM YORP, U-15N, 13C; 20
REMARK 210 MM NH4OAC, 100MM NACL, 10MM DTT,
REMARK 210 5MM CACL2, 0.02% NAN3, 100% D2O;
REMARK 210 0.8MM YORP, U-15N, 5%-13C; 20 MM
REMARK 210 NH4OAC, 100MM NACL, 10MM DTT,
REMARK 210 5MM CACL2, 0.02% NAN3, 95% H2O,
REMARK 210 5% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY; 4D_13C-
REMARK 210 SEPARATED_NOESY; HNHA
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE LINUZ9, VNMR 6.1C,
REMARK 210 AUTOSTRUCTURE 2.1.1
REMARK 210 METHOD USED : SIMULATED ANNEALING, CNS WATER
REMARK 210 REFINEMENT
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 20
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES
REMARK 210 SUBMITTED
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 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 8 -65.03 -163.13
REMARK 500 1 TYR A 9 -73.26 -137.55
REMARK 500 1 ASN A 22 29.91 -78.20
REMARK 500 1 HIS A 79 -41.15 -149.02
REMARK 500 1 HIS A 83 -163.69 61.20
REMARK 500 2 PRO A 5 -84.93 -53.35
REMARK 500 2 LEU A 6 92.76 -168.42
REMARK 500 2 TYR A 9 -122.88 61.65
REMARK 500 2 ASN A 22 90.42 -60.02
REMARK 500 2 ASN A 23 -30.45 72.05
REMARK 500 2 ARG A 25 -93.86 46.24
REMARK 500 2 TYR A 26 96.58 -165.31
REMARK 500 2 CYS A 28 103.28 -179.13
REMARK 500 2 HIS A 30 93.79 -67.01
REMARK 500 2 HIS A 31 -32.86 74.61
REMARK 500 2 HIS A 80 -78.88 -102.91
REMARK 500 2 HIS A 81 -67.99 -92.47
REMARK 500 2 HIS A 82 -70.61 -117.37
REMARK 500 3 ALA A 2 -70.94 178.09
REMARK 500 3 HIS A 31 18.26 -150.89
REMARK 500 3 ALA A 74 31.77 -98.24
REMARK 500 3 HIS A 80 117.79 73.56
REMARK 500 4 ALA A 2 97.70 65.73
REMARK 500 4 HIS A 31 -88.46 -133.48
REMARK 500 4 VAL A 32 -169.57 59.00
REMARK 500 4 HIS A 79 -64.73 -101.52
REMARK 500 5 LEU A 6 102.49 70.07
REMARK 500 5 ASN A 22 24.63 -76.64
REMARK 500 5 CYS A 28 85.70 -164.80
REMARK 500 5 LYS A 70 -77.37 -67.57
REMARK 500 5 TYR A 75 -40.07 -166.67
REMARK 500 5 LEU A 77 -74.63 -96.78
REMARK 500 5 HIS A 81 87.31 60.42
REMARK 500 5 HIS A 83 -71.82 -136.33
REMARK 500 6 TYR A 9 -138.36 -138.59
REMARK 500 6 LYS A 70 -30.76 69.94
REMARK 500 6 GLU A 78 -61.26 -144.42
REMARK 500 6 HIS A 79 45.11 -79.70
REMARK 500 7 LEU A 6 88.35 59.63
REMARK 500 7 PRO A 7 95.21 -69.36
REMARK 500 7 ASN A 22 23.71 -77.52
REMARK 500 7 ALA A 24 31.19 -86.38
REMARK 500 7 CYS A 28 103.79 -166.84
REMARK 500 7 TYR A 75 91.91 73.92
REMARK 500 7 HIS A 82 -67.01 -173.79
REMARK 500 7 HIS A 83 31.83 -155.26
REMARK 500 8 ALA A 2 -71.09 -168.93
REMARK 500 8 PRO A 7 100.41 -59.20
REMARK 500 8 ASN A 22 89.37 -54.24
REMARK 500 8 TYR A 26 82.30 -167.72
REMARK 500
REMARK 500 THIS ENTRY HAS 167 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: SR399 RELATED DB: TARGETDB
DBREF 2HEQ A 7 76 UNP O31898 O31898_BACSU 2 71
SEQADV 2HEQ MET A 1 UNP O31898 CLONING ARTIFACT
SEQADV 2HEQ ALA A 2 UNP O31898 CLONING ARTIFACT
SEQADV 2HEQ GLY A 3 UNP O31898 CLONING ARTIFACT
SEQADV 2HEQ ASP A 4 UNP O31898 CLONING ARTIFACT
SEQADV 2HEQ PRO A 5 UNP O31898 CLONING ARTIFACT
SEQADV 2HEQ LEU A 6 UNP O31898 CLONING ARTIFACT
SEQADV 2HEQ LEU A 77 UNP O31898 CLONING ARTIFACT
SEQADV 2HEQ GLU A 78 UNP O31898 CLONING ARTIFACT
SEQADV 2HEQ HIS A 79 UNP O31898 EXPRESSION TAG
SEQADV 2HEQ HIS A 80 UNP O31898 EXPRESSION TAG
SEQADV 2HEQ HIS A 81 UNP O31898 EXPRESSION TAG
SEQADV 2HEQ HIS A 82 UNP O31898 EXPRESSION TAG
SEQADV 2HEQ HIS A 83 UNP O31898 EXPRESSION TAG
SEQADV 2HEQ HIS A 84 UNP O31898 EXPRESSION TAG
SEQRES 1 A 84 MET ALA GLY ASP PRO LEU PRO LYS TYR TRP SER TYR PRO
SEQRES 2 A 84 VAL GLY LEU ALA VAL GLU ILE ASN ASN ASN ALA ARG TYR
SEQRES 3 A 84 GLY CYS PRO HIS HIS VAL GLY ARG LYS GLY LYS ILE ILE
SEQRES 4 A 84 GLU HIS LEU HIS SER ALA THR TYR ASP TYR ALA VAL SER
SEQRES 5 A 84 ASP GLU THR GLY ASP ILE THR TYR PHE LYS GLU HIS GLU
SEQRES 6 A 84 LEU THR PRO LEU LYS GLY GLY LEU ALA TYR VAL LEU GLU
SEQRES 7 A 84 HIS HIS HIS HIS HIS HIS
HELIX 1 1 LYS A 62 HIS A 64 5 3
SHEET 1 A 5 ILE A 58 PHE A 61 0
SHEET 2 A 5 TYR A 49 ASP A 53 -1 N VAL A 51 O THR A 59
SHEET 3 A 5 LYS A 35 HIS A 41 -1 N LYS A 37 O SER A 52
SHEET 4 A 5 ALA A 17 ILE A 20 -1 N VAL A 18 O GLY A 36
SHEET 5 A 5 LEU A 66 PRO A 68 -1 O THR A 67 N GLU A 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
