HEADER DNA BINDING PROTEIN 14-JUN-05 1ZZK TITLE CRYSTAL STRUCTURE OF THE THIRD KH DOMAIN OF HNRNP K AT 0.95A TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN K; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KH3 DOMAIN; COMPND 5 SYNONYM: HNRNP K, TRANSFORMATION UP-REGULATED NUCLEAR PROTEIN, TUNP; 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: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS KH DOMIAN, ALPHA-BETA FOLD, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.H.BACKE,A.C.MESSIAS,R.B.RAVELLI,M.SATTLER,S.CUSACK REVDAT 3 13-MAR-24 1ZZK 1 SEQADV REVDAT 2 24-FEB-09 1ZZK 1 VERSN REVDAT 1 09-AUG-05 1ZZK 0 JRNL AUTH P.H.BACKE,A.C.MESSIAS,R.B.RAVELLI,M.SATTLER,S.CUSACK JRNL TITL X-RAY CRYSTALLOGRAPHIC AND NMR STUDIES OF THE THIRD KH JRNL TITL 2 DOMAIN OF HNRNP K IN COMPLEX WITH SINGLE-STRANDED NUCLEIC JRNL TITL 3 ACIDS JRNL REF STRUCTURE V. 13 1055 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 16004877 JRNL DOI 10.1016/J.STR.2005.04.008 REMARK 2 REMARK 2 RESOLUTION. 0.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.124 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.124 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.127 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2007 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 40192 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 617 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 58 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.037 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.081 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.123 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.042 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.101 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZZK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033306. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : KHOZU DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40192 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, PEG 400, TRIS-HCL, REMARK 280 PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 25.92400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.43800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.92400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.43800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 8 REMARK 465 ALA A 9 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLY A 55 N C O REMARK 480 GLU A 57 CD OE1 OE2 REMARK 480 LYS A 87 CD CE NZ 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 SER A 27 CB SER A 27 OG -0.079 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 MET A 10 N - CA - CB ANGL. DEV. = -11.0 DEGREES REMARK 500 SER A 27 CA - CB - OG ANGL. DEV. = 17.4 DEGREES REMARK 500 ARG A 35 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 35 NE - CZ - NH2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ILE A 61 CB - CG1 - CD1 ANGL. DEV. = 19.1 DEGREES REMARK 500 GLN A 67 CG - CD - OE1 ANGL. DEV. = 15.2 DEGREES REMARK 500 ASP A 68 CB - CG - OD1 ANGL. DEV. = -8.1 DEGREES REMARK 500 TYR A 75 CB - CG - CD2 ANGL. DEV. = -5.3 DEGREES REMARK 500 TYR A 75 CB - CG - CD1 ANGL. DEV. = 7.7 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 ILE A 29 -66.22 -97.93 REMARK 500 ASP A 50 171.33 -59.04 REMARK 500 GLU A 54 26.44 -71.56 REMARK 500 SER A 56 178.12 34.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZZI RELATED DB: PDB REMARK 900 RELATED ID: 1ZZJ RELATED DB: PDB DBREF 1ZZK A 11 89 UNP P61978 HNRPK_HUMAN 385 463 SEQADV 1ZZK GLY A 8 UNP P61978 CLONING ARTIFACT SEQADV 1ZZK ALA A 9 UNP P61978 CLONING ARTIFACT SEQADV 1ZZK MET A 10 UNP P61978 CLONING ARTIFACT SEQRES 1 A 82 GLY ALA MET GLY PRO ILE ILE THR THR GLN VAL THR ILE SEQRES 2 A 82 PRO LYS ASP LEU ALA GLY SER ILE ILE GLY LYS GLY GLY SEQRES 3 A 82 GLN ARG ILE LYS GLN ILE ARG HIS GLU SER GLY ALA SER SEQRES 4 A 82 ILE LYS ILE ASP GLU PRO LEU GLU GLY SER GLU ASP ARG SEQRES 5 A 82 ILE ILE THR ILE THR GLY THR GLN ASP GLN ILE GLN ASN SEQRES 6 A 82 ALA GLN TYR LEU LEU GLN ASN SER VAL LYS GLN TYR SER SEQRES 7 A 82 GLY LYS PHE PHE FORMUL 2 HOH *58(H2 O) HELIX 1 1 LEU A 24 ILE A 29 5 6 HELIX 2 2 GLY A 30 GLY A 32 5 3 HELIX 3 3 GLY A 33 GLY A 44 1 12 HELIX 4 4 THR A 66 GLY A 86 1 21 SHEET 1 A 3 ILE A 14 PRO A 21 0 SHEET 2 A 3 ASP A 58 GLY A 65 -1 O ILE A 63 N THR A 16 SHEET 3 A 3 SER A 46 ILE A 49 -1 N LYS A 48 O THR A 62 CRYST1 51.848 30.876 42.413 90.00 102.74 90.00 C 1 2 1 4 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 0.019287 0.000000 0.004361 0.00000 SCALE2 0.000000 0.032388 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024173 0.00000