HEADER ANTITOXIN 10-JUN-09 3HS2 TITLE CRYSTAL STRUCTURE OF PHD TRUNCATED TO RESIDUE 57 IN AN ORTHORHOMBIC TITLE 2 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PREVENT HOST DEATH PROTEIN; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN: UNP RESIDUES 1-58; COMPND 5 SYNONYM: PHD PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE P1; SOURCE 3 ORGANISM_COMMON: BACTERIOPHAGE P1; SOURCE 4 ORGANISM_TAXID: 10678; SOURCE 5 GENE: PHD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS PREVENT HOST DEATH, PHD, INTRINSIC DISORDER, DOC, TOXIN-ANTITOXIN, KEYWDS 2 ANTITOXIN EXPDTA X-RAY DIFFRACTION AUTHOR A.GARCIA-PINO,R.LORIS REVDAT 3 06-SEP-23 3HS2 1 REMARK REVDAT 2 21-JUL-10 3HS2 1 JRNL REVDAT 1 23-JUN-10 3HS2 0 JRNL AUTH A.GARCIA-PINO,S.BALASUBRAMANIAN,L.WYNS,E.GAZIT,H.DE GREVE, JRNL AUTH 2 R.D.MAGNUSON,D.CHARLIER,N.A.VAN NULAND,R.LORIS JRNL TITL ALLOSTERY AND INTRINSIC DISORDER MEDIATE TRANSCRIPTION JRNL TITL 2 REGULATION BY CONDITIONAL COOPERATIVITY. JRNL REF CELL(CAMBRIDGE,MASS.) V. 142 101 2010 JRNL REFN ISSN 0092-8674 JRNL PMID 20603017 JRNL DOI 10.1016/J.CELL.2010.05.039 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 20810 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.230 REMARK 3 FREE R VALUE TEST SET COUNT : 1448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.2500 - 4.7361 0.92 1874 146 0.2441 0.2703 REMARK 3 2 4.7361 - 3.7607 0.93 1814 139 0.2053 0.2268 REMARK 3 3 3.7607 - 3.2858 0.98 1935 129 0.2111 0.2419 REMARK 3 4 3.2858 - 2.9855 0.99 1885 154 0.2162 0.2778 REMARK 3 5 2.9855 - 2.7717 0.99 1911 132 0.2287 0.2919 REMARK 3 6 2.7717 - 2.6083 0.98 1866 158 0.2313 0.2922 REMARK 3 7 2.6083 - 2.4777 0.97 1843 148 0.2425 0.3095 REMARK 3 8 2.4777 - 2.3699 0.97 1846 135 0.2367 0.3147 REMARK 3 9 2.3699 - 2.2787 0.96 1813 151 0.2309 0.2948 REMARK 3 10 2.2787 - 2.2000 0.95 1779 156 0.2525 0.3005 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 56.10 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.740 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3HS2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053514. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20810 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 34.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : 0.11000 REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.32100 REMARK 200 R SYM FOR SHELL (I) : 0.32100 REMARK 200 FOR SHELL : 6.870 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3HRY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 0.2M LISO4, 0.1M SODIUM REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 30.58700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.58700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 53.50050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.27100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 53.50050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.27100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.58700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 53.50050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.27100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.58700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 53.50050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.27100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, G 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, G, H 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 ALA A 57 REMARK 465 SER A 58 REMARK 465 ALA B 57 REMARK 465 SER B 58 REMARK 465 ALA D 57 REMARK 465 SER D 58 REMARK 465 GLU E 55 REMARK 465 PHE E 56 REMARK 465 ALA E 57 REMARK 465 SER E 58 REMARK 465 MET F 1 REMARK 465 ALA F 57 REMARK 465 SER F 58 REMARK 465 ASP G 53 REMARK 465 ALA G 54 REMARK 465 GLU G 55 REMARK 465 PHE G 56 REMARK 465 ALA G 57 REMARK 465 SER G 58 REMARK 465 PHE H 56 REMARK 465 ALA H 57 REMARK 465 SER H 58 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 2 CG CD OE1 NE2 REMARK 470 ARG A 7 CZ NH1 NH2 REMARK 470 ARG A 10 CD NE CZ NH1 NH2 REMARK 470 ARG A 31 CD NE CZ NH1 NH2 REMARK 470 LYS A 49 CD CE NZ REMARK 470 ASP A 53 CG OD1 OD2 REMARK 470 GLU A 55 CG CD OE1 OE2 REMARK 470 PHE A 56 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN B 2 CG CD OE1 NE2 REMARK 470 ARG B 10 CD NE CZ NH1 NH2 REMARK 470 GLU B 15 CG CD OE1 OE2 REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 GLU B 25 CD OE1 OE2 REMARK 470 ARG B 31 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 49 CG CD CE NZ REMARK 470 GLU B 55 CG CD OE1 OE2 REMARK 470 ARG C 7 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 31 CG CD NE CZ NH1 NH2 REMARK 470 ASP C 53 CG OD1 OD2 REMARK 470 GLU C 55 CB CG CD OE1 OE2 REMARK 470 PHE C 56 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER C 58 OG REMARK 470 ARG D 7 CD NE CZ NH1 NH2 REMARK 470 ARG D 10 CD NE CZ NH1 NH2 REMARK 470 GLU D 24 CG CD OE1 OE2 REMARK 470 ARG D 31 CD NE CZ NH1 NH2 REMARK 470 GLU D 55 CG CD OE1 OE2 REMARK 470 ILE E 4 CD1 REMARK 470 ARG E 7 CG CD NE CZ NH1 NH2 REMARK 470 ARG E 10 CD NE CZ NH1 NH2 REMARK 470 GLU E 15 CG CD OE1 OE2 REMARK 470 ARG E 31 CZ NH1 NH2 REMARK 470 LYS E 41 CE NZ REMARK 470 LYS E 48 CG CD CE NZ REMARK 470 LYS E 49 CG CD CE NZ REMARK 470 LEU E 52 CG CD1 CD2 REMARK 470 ASP E 53 CG OD1 OD2 REMARK 470 ILE F 4 CD1 REMARK 470 ARG F 7 CG CD NE CZ NH1 NH2 REMARK 470 ARG F 10 CD NE CZ NH1 NH2 REMARK 470 GLU F 15 CD OE1 OE2 REMARK 470 ARG F 31 CD NE CZ NH1 NH2 REMARK 470 GLU F 34 CG CD OE1 OE2 REMARK 470 LYS F 49 CG CD CE NZ REMARK 470 GLU F 55 CG CD OE1 OE2 REMARK 470 ILE G 4 CD1 REMARK 470 ASN G 12 CG OD1 ND2 REMARK 470 GLU G 15 CG CD OE1 OE2 REMARK 470 ARG G 31 CD NE CZ NH1 NH2 REMARK 470 GLN H 2 CD OE1 NE2 REMARK 470 ILE H 4 CD1 REMARK 470 ARG H 7 CG CD NE CZ NH1 NH2 REMARK 470 GLU H 15 CG CD OE1 OE2 REMARK 470 ARG H 31 CG CD NE CZ NH1 NH2 REMARK 470 GLU H 34 CG CD OE1 OE2 REMARK 470 LYS H 49 CG CD CE NZ REMARK 470 LEU H 52 CD1 CD2 REMARK 470 GLU H 55 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 HOH D 81 O HOH D 85 2.19 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 ALA C 57 CB - CA - C ANGL. DEV. = -17.1 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 ASN H 12 33.30 -142.14 REMARK 500 ASP H 53 -70.99 -49.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 F 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 G 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 107 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HRY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FULL LENGTH PHD FROM BACTERIOPHAGE P1 REMARK 900 RELATED ID: 3DD7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF PHD DBREF 3HS2 A 1 58 UNP Q06253 PHD_BPP1 1 58 DBREF 3HS2 B 1 58 UNP Q06253 PHD_BPP1 1 58 DBREF 3HS2 C 1 58 UNP Q06253 PHD_BPP1 1 58 DBREF 3HS2 D 1 58 UNP Q06253 PHD_BPP1 1 58 DBREF 3HS2 E 1 58 UNP Q06253 PHD_BPP1 1 58 DBREF 3HS2 F 1 58 UNP Q06253 PHD_BPP1 1 58 DBREF 3HS2 G 1 58 UNP Q06253 PHD_BPP1 1 58 DBREF 3HS2 H 1 58 UNP Q06253 PHD_BPP1 1 58 SEQRES 1 A 58 MET GLN SER ILE ASN PHE ARG THR ALA ARG GLY ASN LEU SEQRES 2 A 58 SER GLU VAL LEU ASN ASN VAL GLU ALA GLY GLU GLU VAL SEQRES 3 A 58 GLU ILE THR ARG ARG GLY ARG GLU PRO ALA VAL ILE VAL SEQRES 4 A 58 SER LYS ALA THR PHE GLU ALA TYR LYS LYS ALA ALA LEU SEQRES 5 A 58 ASP ALA GLU PHE ALA SER SEQRES 1 B 58 MET GLN SER ILE ASN PHE ARG THR ALA ARG GLY ASN LEU SEQRES 2 B 58 SER GLU VAL LEU ASN ASN VAL GLU ALA GLY GLU GLU VAL SEQRES 3 B 58 GLU ILE THR ARG ARG GLY ARG GLU PRO ALA VAL ILE VAL SEQRES 4 B 58 SER LYS ALA THR PHE GLU ALA TYR LYS LYS ALA ALA LEU SEQRES 5 B 58 ASP ALA GLU PHE ALA SER SEQRES 1 C 58 MET GLN SER ILE ASN PHE ARG THR ALA ARG GLY ASN LEU SEQRES 2 C 58 SER GLU VAL LEU ASN ASN VAL GLU ALA GLY GLU GLU VAL SEQRES 3 C 58 GLU ILE THR ARG ARG GLY ARG GLU PRO ALA VAL ILE VAL SEQRES 4 C 58 SER LYS ALA THR PHE GLU ALA TYR LYS LYS ALA ALA LEU SEQRES 5 C 58 ASP ALA GLU PHE ALA SER SEQRES 1 D 58 MET GLN SER ILE ASN PHE ARG THR ALA ARG GLY ASN LEU SEQRES 2 D 58 SER GLU VAL LEU ASN ASN VAL GLU ALA GLY GLU GLU VAL SEQRES 3 D 58 GLU ILE THR ARG ARG GLY ARG GLU PRO ALA VAL ILE VAL SEQRES 4 D 58 SER LYS ALA THR PHE GLU ALA TYR LYS LYS ALA ALA LEU SEQRES 5 D 58 ASP ALA GLU PHE ALA SER SEQRES 1 E 58 MET GLN SER ILE ASN PHE ARG THR ALA ARG GLY ASN LEU SEQRES 2 E 58 SER GLU VAL LEU ASN ASN VAL GLU ALA GLY GLU GLU VAL SEQRES 3 E 58 GLU ILE THR ARG ARG GLY ARG GLU PRO ALA VAL ILE VAL SEQRES 4 E 58 SER LYS ALA THR PHE GLU ALA TYR LYS LYS ALA ALA LEU SEQRES 5 E 58 ASP ALA GLU PHE ALA SER SEQRES 1 F 58 MET GLN SER ILE ASN PHE ARG THR ALA ARG GLY ASN LEU SEQRES 2 F 58 SER GLU VAL LEU ASN ASN VAL GLU ALA GLY GLU GLU VAL SEQRES 3 F 58 GLU ILE THR ARG ARG GLY ARG GLU PRO ALA VAL ILE VAL SEQRES 4 F 58 SER LYS ALA THR PHE GLU ALA TYR LYS LYS ALA ALA LEU SEQRES 5 F 58 ASP ALA GLU PHE ALA SER SEQRES 1 G 58 MET GLN SER ILE ASN PHE ARG THR ALA ARG GLY ASN LEU SEQRES 2 G 58 SER GLU VAL LEU ASN ASN VAL GLU ALA GLY GLU GLU VAL SEQRES 3 G 58 GLU ILE THR ARG ARG GLY ARG GLU PRO ALA VAL ILE VAL SEQRES 4 G 58 SER LYS ALA THR PHE GLU ALA TYR LYS LYS ALA ALA LEU SEQRES 5 G 58 ASP ALA GLU PHE ALA SER SEQRES 1 H 58 MET GLN SER ILE ASN PHE ARG THR ALA ARG GLY ASN LEU SEQRES 2 H 58 SER GLU VAL LEU ASN ASN VAL GLU ALA GLY GLU GLU VAL SEQRES 3 H 58 GLU ILE THR ARG ARG GLY ARG GLU PRO ALA VAL ILE VAL SEQRES 4 H 58 SER LYS ALA THR PHE GLU ALA TYR LYS LYS ALA ALA LEU SEQRES 5 H 58 ASP ALA GLU PHE ALA SER HET SO4 B 106 5 HET SO4 C 102 5 HET SO4 D 101 5 HET SO4 F 103 5 HET SO4 G 105 5 HET SO4 H 107 5 HETNAM SO4 SULFATE ION FORMUL 9 SO4 6(O4 S 2-) FORMUL 15 HOH *83(H2 O) HELIX 1 1 PHE A 6 ASN A 12 1 7 HELIX 2 2 ASN A 12 ALA A 22 1 11 HELIX 3 3 LYS A 41 PHE A 56 1 16 HELIX 4 4 PHE B 6 ASN B 12 1 7 HELIX 5 5 ASN B 12 ALA B 22 1 11 HELIX 6 6 LYS B 41 PHE B 56 1 16 HELIX 7 7 PHE C 6 ASN C 12 1 7 HELIX 8 8 ASN C 12 ALA C 22 1 11 HELIX 9 9 LYS C 41 GLU C 55 1 15 HELIX 10 10 PHE D 6 ALA D 22 1 17 HELIX 11 11 LYS D 41 PHE D 56 1 16 HELIX 12 12 PHE E 6 ASN E 12 1 7 HELIX 13 13 ASN E 12 ALA E 22 1 11 HELIX 14 14 LYS E 41 ASP E 53 1 13 HELIX 15 15 PHE F 6 ASN F 12 1 7 HELIX 16 16 ASN F 12 ALA F 22 1 11 HELIX 17 17 LYS F 41 PHE F 56 1 16 HELIX 18 18 PHE G 6 ASN G 12 1 7 HELIX 19 19 ASN G 12 ALA G 22 1 11 HELIX 20 20 LYS G 41 LEU G 52 1 12 HELIX 21 21 PHE H 6 ASN H 12 1 7 HELIX 22 22 ASN H 12 ALA H 22 1 11 HELIX 23 23 LYS H 41 ALA H 54 1 14 SHEET 1 A 6 GLN A 2 ASN A 5 0 SHEET 2 A 6 VAL A 26 THR A 29 1 O GLU A 27 N GLN A 2 SHEET 3 A 6 ALA A 36 SER A 40 -1 O ALA A 36 N ILE A 28 SHEET 4 A 6 ARG B 33 SER B 40 -1 O VAL B 37 N VAL A 39 SHEET 5 A 6 VAL B 26 ARG B 30 -1 N ILE B 28 O ALA B 36 SHEET 6 A 6 GLN B 2 ASN B 5 1 N ILE B 4 O GLU B 27 SHEET 1 B 6 GLN C 2 ASN C 5 0 SHEET 2 B 6 VAL C 26 THR C 29 1 O GLU C 27 N GLN C 2 SHEET 3 B 6 ALA C 36 SER C 40 -1 O ILE C 38 N VAL C 26 SHEET 4 B 6 ALA D 36 SER D 40 -1 O VAL D 37 N VAL C 39 SHEET 5 B 6 VAL D 26 THR D 29 -1 N ILE D 28 O ALA D 36 SHEET 6 B 6 GLN D 2 ASN D 5 1 N GLN D 2 O GLU D 27 SHEET 1 C 6 GLN E 2 ASN E 5 0 SHEET 2 C 6 VAL E 26 THR E 29 1 O GLU E 27 N ILE E 4 SHEET 3 C 6 ALA E 36 SER E 40 -1 O ALA E 36 N ILE E 28 SHEET 4 C 6 ALA F 36 SER F 40 -1 O VAL F 37 N VAL E 39 SHEET 5 C 6 VAL F 26 THR F 29 -1 N ILE F 28 O ALA F 36 SHEET 6 C 6 SER F 3 ASN F 5 1 N ILE F 4 O THR F 29 SHEET 1 D 6 GLN G 2 ASN G 5 0 SHEET 2 D 6 VAL G 26 THR G 29 1 O GLU G 27 N GLN G 2 SHEET 3 D 6 ALA G 36 SER G 40 -1 O ILE G 38 N VAL G 26 SHEET 4 D 6 ALA H 36 SER H 40 -1 O VAL H 39 N VAL G 37 SHEET 5 D 6 VAL H 26 THR H 29 -1 N ILE H 28 O ALA H 36 SHEET 6 D 6 GLN H 2 ASN H 5 1 N ILE H 4 O GLU H 27 CISPEP 1 GLU C 55 PHE C 56 0 7.52 SITE 1 AC1 2 ASN B 12 ASN B 19 SITE 1 AC2 6 ASN C 5 PHE C 6 ARG C 7 THR C 29 SITE 2 AC2 6 ARG C 30 ARG C 31 SITE 1 AC3 6 ASN D 5 PHE D 6 ARG D 7 THR D 29 SITE 2 AC3 6 ARG D 30 ARG D 31 SITE 1 AC4 4 ASN F 5 PHE F 6 ARG F 7 THR F 29 SITE 1 AC5 5 ASN G 5 PHE G 6 ARG G 7 THR G 29 SITE 2 AC5 5 ARG G 31 SITE 1 AC6 1 ASN H 12 CRYST1 107.001 122.542 61.174 90.00 90.00 90.00 C 2 2 21 64 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 0.009346 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008160 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016347 0.00000