PDB Short entry for 2BZE HEADER TRANSCRIPTION REGULATION 16-AUG-05 2BZE TITLE NMR STRUCTURE OF HUMAN RTF1 PLUS3 DOMAIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: KIAA0252 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PLUS3, RESIDUES 228-359; COMPND 5 SYNONYM: RFT1 PLUS3 DOMAIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 OTHER_DETAILS: SELF MADE CDNA LIBRARY OF MULTIPLE HUMAN CARCINOMA SOURCE 11 CELL LINES KEYWDS HUMAN RTF1 PLUS3 DOMAIN, TRANSCRIPTION, ELONGATION, PAF1 COMPLEX, KEYWDS 2 HISTONE H3 METHYLATION, H2B UBIQUITINATION, CDC73, LEO1, CTR9, PLUS3 KEYWDS 3 DOMAIN, TRANSCRIPTION REGULATION, STRUCTURAL PROTEOMICS IN EUROPE, KEYWDS 4 SPINE, STRUCTURAL GENOMICS EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR V.TRUFFAULT,T.DIERCKS,E.AB,R.N.DE JONG,M.A.DANIELS,R.KAPTEIN, AUTHOR 2 G.E.FOLKERS,STRUCTURAL PROTEOMICS IN EUROPE (SPINE) REVDAT 6 14-JUN-23 2BZE 1 REMARK REVDAT 5 15-JAN-20 2BZE 1 REMARK REVDAT 4 24-MAY-17 2BZE 1 AUTHOR REVDAT 3 24-FEB-09 2BZE 1 VERSN REVDAT 2 22-JAN-08 2BZE 1 AUTHOR JRNL REVDAT 1 03-JAN-07 2BZE 0 JRNL AUTH R.N.DE JONG,V.TRUFFAULT,T.DIERCKS,E.AB,M.A.DANIELS, JRNL AUTH 2 R.KAPTEIN,G.E.FOLKERS JRNL TITL STRUCTURE AND DNA BINDING OF THE HUMAN RTF1 PLUS3 DOMAIN. JRNL REF STRUCTURE V. 16 149 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18184592 JRNL DOI 10.1016/J.STR.2007.10.018 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WATER REFINEMENT ACCORDING TO RECORD REMARK 3 PROTOCOL REMARK 4 REMARK 4 2BZE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1290025340. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 200 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 90% WATER/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCO; HNH-NOESY; HCH-NOESY; CNH REMARK 210 -NOESY; HH-NOESY; HNCACO; HNCACB; REMARK 210 CBCACONH; HBHACONH; HNCAHA; CCH- REMARK 210 COSY; HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, CYANA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOW ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NONE 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-25 REMARK 470 RES CSSEQI ATOMS REMARK 470 ASN A 476 O 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 7 TYR A 407 CG TYR A 407 CD1 -0.083 REMARK 500 15 THR A 412 N THR A 412 CA -0.124 REMARK 500 23 TYR A 407 CG TYR A 407 CD1 -0.085 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 7 TYR A 407 CB - CG - CD2 ANGL. DEV. = 3.8 DEGREES REMARK 500 7 TYR A 407 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 23 TYR A 407 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES 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 HIS A -17 -175.67 70.34 REMARK 500 1 ARG A -5 -80.79 61.56 REMARK 500 1 PRO A 368 -164.94 -60.51 REMARK 500 1 PHE A 369 80.41 -58.44 REMARK 500 1 HIS A 386 -38.57 173.73 REMARK 500 1 SER A 388 -61.68 69.36 REMARK 500 1 PRO A 390 87.42 -66.44 REMARK 500 1 ASN A 415 51.93 -110.41 REMARK 500 2 HIS A -16 -37.39 72.17 REMARK 500 2 HIS A -14 -82.47 62.78 REMARK 500 2 HIS A -12 -76.72 -84.68 REMARK 500 2 SER A -3 -29.03 -170.79 REMARK 500 2 PRO A 368 -165.10 -76.88 REMARK 500 2 HIS A 386 -51.60 -165.24 REMARK 500 2 SER A 388 -39.51 -155.81 REMARK 500 2 ASN A 415 50.19 -105.41 REMARK 500 3 HIS A -15 -77.96 -142.01 REMARK 500 3 SER A -10 -56.71 73.22 REMARK 500 3 HIS A -2 -173.25 -177.70 REMARK 500 3 PRO A 368 -165.61 -63.45 REMARK 500 3 HIS A 386 -162.59 -103.38 REMARK 500 3 ASN A 415 52.76 -98.76 REMARK 500 4 SER A -18 -3.63 70.74 REMARK 500 4 HIS A -17 171.58 71.21 REMARK 500 4 HIS A -12 84.02 56.60 REMARK 500 4 MET A -1 173.60 60.21 REMARK 500 4 PRO A 368 -165.01 -67.19 REMARK 500 4 PHE A 369 104.33 -58.99 REMARK 500 4 ASN A 387 -157.90 -101.09 REMARK 500 4 ASN A 415 51.11 -103.09 REMARK 500 5 SER A -18 -67.21 -150.07 REMARK 500 5 HIS A -17 79.75 60.77 REMARK 500 5 HIS A -13 66.40 68.63 REMARK 500 5 HIS A -12 19.17 -156.62 REMARK 500 5 SER A -11 81.08 -61.66 REMARK 500 5 SER A -10 88.23 157.07 REMARK 500 5 SER A -3 0.41 -67.45 REMARK 500 5 MET A -1 156.39 63.51 REMARK 500 5 HIS A 366 -25.81 175.12 REMARK 500 5 PRO A 368 -166.38 -65.20 REMARK 500 5 ILE A 383 78.44 -116.41 REMARK 500 5 ASN A 415 63.98 -102.18 REMARK 500 6 HIS A -16 -66.23 72.80 REMARK 500 6 HIS A -15 -60.69 152.71 REMARK 500 6 LEU A -8 93.26 60.73 REMARK 500 6 PRO A 368 -164.96 -71.59 REMARK 500 6 ILE A 383 79.74 -105.68 REMARK 500 6 ASN A 415 52.35 -99.52 REMARK 500 7 HIS A -16 -98.34 -93.89 REMARK 500 7 HIS A -12 -40.40 -152.91 REMARK 500 REMARK 500 THIS ENTRY HAS 164 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 410 GLY A 411 1 -146.12 REMARK 500 GLY A 410 GLY A 411 2 -142.07 REMARK 500 GLY A 410 GLY A 411 3 -147.75 REMARK 500 GLY A 410 GLY A 411 4 -147.05 REMARK 500 GLY A 410 GLY A 411 5 -144.42 REMARK 500 GLY A 410 GLY A 411 6 -148.10 REMARK 500 GLY A 410 GLY A 411 7 -145.03 REMARK 500 GLY A 410 GLY A 411 8 -139.26 REMARK 500 GLY A 410 GLY A 411 9 -146.68 REMARK 500 GLY A 410 GLY A 411 10 -146.33 REMARK 500 GLY A 410 GLY A 411 11 -142.30 REMARK 500 GLY A 410 GLY A 411 12 -148.03 REMARK 500 GLY A 410 GLY A 411 13 -149.65 REMARK 500 GLY A 410 GLY A 411 14 -146.22 REMARK 500 GLY A 410 GLY A 411 15 -145.73 REMARK 500 GLY A 410 GLY A 411 16 -140.03 REMARK 500 GLY A 410 GLY A 411 17 -145.39 REMARK 500 GLY A 410 GLY A 411 18 -144.07 REMARK 500 GLY A 410 GLY A 411 19 -148.04 REMARK 500 GLY A 410 GLY A 411 20 -146.90 REMARK 500 GLY A 410 GLY A 411 21 -147.65 REMARK 500 GLY A 410 GLY A 411 23 -145.73 REMARK 500 GLY A 410 GLY A 411 24 -147.04 REMARK 500 GLY A 410 GLY A 411 25 -147.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 3 ARG A 353 0.09 SIDE CHAIN REMARK 500 3 ARG A 421 0.08 SIDE CHAIN REMARK 500 4 ARG A 353 0.08 SIDE CHAIN REMARK 500 4 ARG A 421 0.08 SIDE CHAIN REMARK 500 4 ARG A 427 0.08 SIDE CHAIN REMARK 500 5 ARG A 353 0.08 SIDE CHAIN REMARK 500 7 ARG A 353 0.08 SIDE CHAIN REMARK 500 9 ARG A 353 0.09 SIDE CHAIN REMARK 500 10 ARG A 380 0.12 SIDE CHAIN REMARK 500 10 ARG A 421 0.09 SIDE CHAIN REMARK 500 11 ARG A 353 0.08 SIDE CHAIN REMARK 500 13 ARG A 380 0.09 SIDE CHAIN REMARK 500 16 ARG A 353 0.08 SIDE CHAIN REMARK 500 16 ARG A 363 0.07 SIDE CHAIN REMARK 500 18 ARG A 427 0.13 SIDE CHAIN REMARK 500 19 ARG A -5 0.09 SIDE CHAIN REMARK 500 22 ARG A 421 0.07 SIDE CHAIN REMARK 500 23 ARG A 380 0.09 SIDE CHAIN REMARK 500 24 ARG A 421 0.07 SIDE CHAIN REMARK 500 25 ARG A 353 0.08 SIDE CHAIN REMARK 500 25 ARG A 427 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7351 RELATED DB: BMRB DBREF 2BZE A -21 -1 PDB 2BZE 2BZE -21 -1 DBREF 2BZE A 345 476 UNP Q92541 Q92541_HUMAN 228 359 SEQRES 1 A 153 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 153 LEU VAL PRO ARG GLY SER HIS MET VAL SER LEU PRO GLU SEQRES 3 A 153 GLU LEU ASN ARG VAL ARG LEU SER ARG HIS LYS LEU GLU SEQRES 4 A 153 ARG TRP CYS HIS MET PRO PHE PHE ALA LYS THR VAL THR SEQRES 5 A 153 GLY CYS PHE VAL ARG ILE GLY ILE GLY ASN HIS ASN SER SEQRES 6 A 153 LYS PRO VAL TYR ARG VAL ALA GLU ILE THR GLY VAL VAL SEQRES 7 A 153 GLU THR ALA LYS VAL TYR GLN LEU GLY GLY THR ARG THR SEQRES 8 A 153 ASN LYS GLY LEU GLN LEU ARG HIS GLY ASN ASP GLN ARG SEQRES 9 A 153 VAL PHE ARG LEU GLU PHE VAL SER ASN GLN GLU PHE THR SEQRES 10 A 153 GLU SER GLU PHE MET LYS TRP LYS GLU ALA MET PHE SER SEQRES 11 A 153 ALA GLY MET GLN LEU PRO THR LEU ASP GLU ILE ASN LYS SEQRES 12 A 153 LYS GLU LEU SER ILE LYS GLU ALA LEU ASN HELIX 1 1 LEU A 347 VAL A 354 1 8 HELIX 2 2 SER A 357 CYS A 365 1 9 HELIX 3 3 PHE A 370 THR A 375 1 6 HELIX 4 4 ARG A 430 PHE A 433 5 4 HELIX 5 5 THR A 440 GLY A 455 1 16 HELIX 6 6 THR A 460 LEU A 475 1 16 SHEET 1 AA 5 ARG A 355 LEU A 356 0 SHEET 2 AA 5 PHE A 378 GLY A 382 1 O PHE A 378 N LEU A 356 SHEET 3 AA 5 TYR A 392 LEU A 409 -1 O ARG A 393 N ILE A 381 SHEET 4 AA 5 THR A 412 ARG A 421 -1 O THR A 412 N LEU A 409 SHEET 5 AA 5 GLN A 426 PHE A 429 -1 O ARG A 427 N LEU A 420 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