HEADER PROTEIN BINDING 20-OCT-22 8BDU TITLE H33 VARIANT OF DOBI SCAFFOLD BASED ON PIH1D1 N-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIH1 DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NUCLEOLAR PROTEIN 17 HOMOLOG; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PIH1D1, NOP17; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTEIN-PROTEIN RECOGNITION, RIBOSOME DISPLAY, IL-10, CYTOKINE, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR P.KOLENKO,P.MIKULECKY,P.N.PHAM,B.SCHNEIDER REVDAT 2 23-AUG-23 8BDU 1 JRNL REVDAT 1 16-AUG-23 8BDU 0 JRNL AUTH P.KOLENKO,P.MIKULECKY,P.N.PHAM,M.MALY,B.SCHNEIDER JRNL TITL DIFFRACTION ANISOTROPY AND PAIRED REFINEMENT: CRYSTAL JRNL TITL 2 STRUCTURE OF H33, A PROTEIN BINDER TO INTERLEUKIN 10. JRNL REF J.APPL.CRYSTALLOGR. V. 56 1261 2023 JRNL REFN ISSN 0021-8898 JRNL PMID 37555209 JRNL DOI 10.1107/S160057672300479X REMARK 2 REMARK 2 RESOLUTION. 2.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 69.2 REMARK 3 NUMBER OF REFLECTIONS : 18374 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM SELECTION REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 910 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 106 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 5.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.4940 REMARK 3 BIN FREE R VALUE SET COUNT : 0 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2071 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.29900 REMARK 3 B22 (A**2) : 0.29900 REMARK 3 B33 (A**2) : -0.59900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.281 REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.252 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.215 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2122 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1910 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2874 ; 1.755 ; 1.639 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4479 ; 0.572 ; 1.551 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 264 ; 6.366 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 12 ;10.028 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 356 ;20.435 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 306 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2411 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 409 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 435 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 43 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1059 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 24 ; 0.115 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1062 ; 9.921 ; 8.108 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1062 ; 9.896 ; 8.110 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1324 ;14.037 ;12.201 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1325 ;14.056 ;12.206 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1060 ; 9.466 ; 8.670 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1061 ; 9.462 ; 8.677 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1550 ;13.481 ;12.742 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1551 ;13.477 ;12.749 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS, THE LAST CYCLES OF REFINEMENT PERFORMED USING REMARK 3 ALL REFLECTIONS. REMARK 4 REMARK 4 8BDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292125846. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976260 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18374 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.470 REMARK 200 RESOLUTION RANGE LOW (A) : 47.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 69.0 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 14.8 REMARK 200 DATA REDUNDANCY IN SHELL : 12.60 REMARK 200 R MERGE FOR SHELL (I) : 3.42900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 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: 7AVC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M (NH4)2SO4 1% (W/V) PEG3350 0.1 M REMARK 280 BIS-TRIS, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 61.56550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 61.56550 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 95.05300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 61.56550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.52650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 61.56550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 142.57950 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 61.56550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 142.57950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.56550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.52650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 61.56550 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 61.56550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 95.05300 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 61.56550 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 61.56550 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 95.05300 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 61.56550 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 142.57950 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 61.56550 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 47.52650 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 61.56550 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 47.52650 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 61.56550 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 142.57950 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 61.56550 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 61.56550 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 95.05300 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 TRP A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 PRO A 6 REMARK 465 GLN A 7 REMARK 465 PHE A 8 REMARK 465 GLU A 9 REMARK 465 LYS A 10 REMARK 465 SER A 11 REMARK 465 SER A 147 REMARK 465 GLN A 148 REMARK 465 GLN A 149 REMARK 465 ASN A 150 REMARK 465 ILE A 151 REMARK 465 ARG A 152 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 TRP B 3 REMARK 465 SER B 4 REMARK 465 HIS B 5 REMARK 465 PRO B 6 REMARK 465 GLN B 7 REMARK 465 PHE B 8 REMARK 465 GLU B 9 REMARK 465 LYS B 10 REMARK 465 PHE B 142 REMARK 465 MET B 143 REMARK 465 GLY B 144 REMARK 465 SER B 145 REMARK 465 ILE B 146 REMARK 465 SER B 147 REMARK 465 GLN B 148 REMARK 465 GLN B 149 REMARK 465 ASN B 150 REMARK 465 ILE B 151 REMARK 465 ARG B 152 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 GLN A 19 -77.61 -59.05 REMARK 500 PRO A 21 155.28 -48.98 REMARK 500 ALA A 67 44.81 -104.85 REMARK 500 ARG A 127 70.70 41.57 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 ARG A 111 0.10 SIDE CHAIN REMARK 500 ARG A 140 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7AVC RELATED DB: PDB REMARK 900 DIFFERENT BINDER VARIANT DBREF 8BDU A 23 152 UNP Q9NWS0 PIHD1_HUMAN 51 180 DBREF 8BDU B 23 152 UNP Q9NWS0 PIHD1_HUMAN 51 180 SEQADV 8BDU MET A 1 UNP Q9NWS0 INITIATING METHIONINE SEQADV 8BDU ALA A 2 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU TRP A 3 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU SER A 4 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU HIS A 5 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU PRO A 6 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU GLN A 7 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU PHE A 8 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU GLU A 9 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU LYS A 10 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU SER A 11 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU ALA A 12 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU ALA A 13 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU LEU A 14 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU GLU A 15 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU VAL A 16 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU LEU A 17 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU PHE A 18 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU GLN A 19 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU GLY A 20 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU PRO A 21 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU GLY A 22 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU TYR A 112 UNP Q9NWS0 GLU 140 ENGINEERED MUTATION SEQADV 8BDU SER A 116 UNP Q9NWS0 THR 144 ENGINEERED MUTATION SEQADV 8BDU ALA A 119 UNP Q9NWS0 ARG 147 ENGINEERED MUTATION SEQADV 8BDU SER A 120 UNP Q9NWS0 GLU 148 ENGINEERED MUTATION SEQADV 8BDU SER A 124 UNP Q9NWS0 ASP 152 ENGINEERED MUTATION SEQADV 8BDU ARG A 127 UNP Q9NWS0 ASN 155 ENGINEERED MUTATION SEQADV 8BDU SER A 129 UNP Q9NWS0 GLN 157 ENGINEERED MUTATION SEQADV 8BDU SER A 131 UNP Q9NWS0 ASN 159 ENGINEERED MUTATION SEQADV 8BDU ILE A 133 UNP Q9NWS0 GLU 161 ENGINEERED MUTATION SEQADV 8BDU TRP A 135 UNP Q9NWS0 ARG 163 ENGINEERED MUTATION SEQADV 8BDU MET B 1 UNP Q9NWS0 INITIATING METHIONINE SEQADV 8BDU ALA B 2 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU TRP B 3 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU SER B 4 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU HIS B 5 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU PRO B 6 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU GLN B 7 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU PHE B 8 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU GLU B 9 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU LYS B 10 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU SER B 11 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU ALA B 12 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU ALA B 13 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU LEU B 14 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU GLU B 15 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU VAL B 16 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU LEU B 17 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU PHE B 18 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU GLN B 19 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU GLY B 20 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU PRO B 21 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU GLY B 22 UNP Q9NWS0 EXPRESSION TAG SEQADV 8BDU TYR B 112 UNP Q9NWS0 GLU 140 ENGINEERED MUTATION SEQADV 8BDU SER B 116 UNP Q9NWS0 THR 144 ENGINEERED MUTATION SEQADV 8BDU ALA B 119 UNP Q9NWS0 ARG 147 ENGINEERED MUTATION SEQADV 8BDU SER B 120 UNP Q9NWS0 GLU 148 ENGINEERED MUTATION SEQADV 8BDU SER B 124 UNP Q9NWS0 ASP 152 ENGINEERED MUTATION SEQADV 8BDU ARG B 127 UNP Q9NWS0 ASN 155 ENGINEERED MUTATION SEQADV 8BDU SER B 129 UNP Q9NWS0 GLN 157 ENGINEERED MUTATION SEQADV 8BDU SER B 131 UNP Q9NWS0 ASN 159 ENGINEERED MUTATION SEQADV 8BDU ILE B 133 UNP Q9NWS0 GLU 161 ENGINEERED MUTATION SEQADV 8BDU TRP B 135 UNP Q9NWS0 ARG 163 ENGINEERED MUTATION SEQRES 1 A 152 MET ALA TRP SER HIS PRO GLN PHE GLU LYS SER ALA ALA SEQRES 2 A 152 LEU GLU VAL LEU PHE GLN GLY PRO GLY GLN PRO GLY PHE SEQRES 3 A 152 CYS ILE LYS THR ASN SER SER GLU GLY LYS VAL PHE ILE SEQRES 4 A 152 ASN ILE CYS HIS SER PRO SER ILE PRO PRO PRO ALA ASP SEQRES 5 A 152 VAL THR GLU GLU GLU LEU LEU GLN MET LEU GLU GLU ASP SEQRES 6 A 152 GLN ALA GLY PHE ARG ILE PRO MET SER LEU GLY GLU PRO SEQRES 7 A 152 HIS ALA GLU LEU ASP ALA LYS GLY GLN GLY CYS THR ALA SEQRES 8 A 152 TYR ASP VAL ALA VAL ASN SER ASP PHE TYR ARG ARG MET SEQRES 9 A 152 GLN ASN SER ASP PHE LEU ARG TYR LEU VAL ILE SER ILE SEQRES 10 A 152 ALA ALA SER GLY LEU GLU SER LYS TYR ARG LEU SER LEU SEQRES 11 A 152 SER PRO ILE TRP TRP MET MET LYS ASN ARG PRO PHE MET SEQRES 12 A 152 GLY SER ILE SER GLN GLN ASN ILE ARG SEQRES 1 B 152 MET ALA TRP SER HIS PRO GLN PHE GLU LYS SER ALA ALA SEQRES 2 B 152 LEU GLU VAL LEU PHE GLN GLY PRO GLY GLN PRO GLY PHE SEQRES 3 B 152 CYS ILE LYS THR ASN SER SER GLU GLY LYS VAL PHE ILE SEQRES 4 B 152 ASN ILE CYS HIS SER PRO SER ILE PRO PRO PRO ALA ASP SEQRES 5 B 152 VAL THR GLU GLU GLU LEU LEU GLN MET LEU GLU GLU ASP SEQRES 6 B 152 GLN ALA GLY PHE ARG ILE PRO MET SER LEU GLY GLU PRO SEQRES 7 B 152 HIS ALA GLU LEU ASP ALA LYS GLY GLN GLY CYS THR ALA SEQRES 8 B 152 TYR ASP VAL ALA VAL ASN SER ASP PHE TYR ARG ARG MET SEQRES 9 B 152 GLN ASN SER ASP PHE LEU ARG TYR LEU VAL ILE SER ILE SEQRES 10 B 152 ALA ALA SER GLY LEU GLU SER LYS TYR ARG LEU SER LEU SEQRES 11 B 152 SER PRO ILE TRP TRP MET MET LYS ASN ARG PRO PHE MET SEQRES 12 B 152 GLY SER ILE SER GLN GLN ASN ILE ARG HELIX 1 AA1 THR A 54 ASP A 65 1 12 HELIX 2 AA2 SER A 98 ASN A 106 1 9 HELIX 3 AA3 SER A 107 TYR A 126 1 20 HELIX 4 AA4 THR B 54 GLU B 64 1 11 HELIX 5 AA5 SER B 98 ASN B 106 1 9 HELIX 6 AA6 SER B 107 ARG B 127 1 21 SHEET 1 AA1 2 ALA A 13 GLU A 15 0 SHEET 2 AA1 2 ILE A 71 MET A 73 1 O ILE A 71 N LEU A 14 SHEET 1 AA2 5 HIS A 79 LEU A 82 0 SHEET 2 AA2 5 GLY A 88 ASN A 97 -1 O ALA A 91 N HIS A 79 SHEET 3 AA2 5 LYS A 36 SER A 44 1 N ASN A 40 O TYR A 92 SHEET 4 AA2 5 GLN A 23 ASN A 31 -1 N THR A 30 O VAL A 37 SHEET 5 AA2 5 TRP A 135 MET A 136 -1 O TRP A 135 N LYS A 29 SHEET 1 AA3 2 ALA B 13 GLU B 15 0 SHEET 2 AA3 2 ILE B 71 MET B 73 1 O ILE B 71 N LEU B 14 SHEET 1 AA4 5 HIS B 79 LEU B 82 0 SHEET 2 AA4 5 GLY B 88 ASN B 97 -1 O CYS B 89 N GLU B 81 SHEET 3 AA4 5 GLY B 35 SER B 44 1 N ASN B 40 O TYR B 92 SHEET 4 AA4 5 GLN B 23 SER B 32 -1 N ILE B 28 O ILE B 39 SHEET 5 AA4 5 TRP B 135 MET B 137 -1 O TRP B 135 N LYS B 29 CISPEP 1 GLY A 20 PRO A 21 0 -9.63 CISPEP 2 GLY B 20 PRO B 21 0 -17.99 CRYST1 123.131 123.131 190.106 90.00 90.00 90.00 I 41 2 2 32 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 0.008121 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008121 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005260 0.00000