PDB Short entry for 2NVH HEADER CYTOKINE 12-NOV-06 2NVH TITLE DETERMINATION OF SOLVENT CONTENT IN CAVITIES IN INTERLEUKIN-1 USING TITLE 2 EXPERIMENTALLY-PHASED ELECTRON DENSITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-1 BETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IL-1 BETA; CATABOLIN; 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: IL1B, IL1F2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS WATER; HYDRATION; PROTEIN FOLDING, CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR M.L.QUILLIN,B.W.MATTHEWS REVDAT 5 30-AUG-23 2NVH 1 REMARK REVDAT 4 18-OCT-17 2NVH 1 REMARK REVDAT 3 24-FEB-09 2NVH 1 VERSN REVDAT 2 09-JAN-07 2NVH 1 JRNL REVDAT 1 12-DEC-06 2NVH 0 JRNL AUTH M.L.QUILLIN,P.T.WINGFIELD,B.W.MATTHEWS JRNL TITL DETERMINATION OF SOLVENT CONTENT IN CAVITIES IN IL-1BETA JRNL TITL 2 USING EXPERIMENTALLY PHASED ELECTRON DENSITY JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 19749 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 17179045 JRNL DOI 10.1073/PNAS.0609442104 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 35225 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NONE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2110 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 35287 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1212 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 149 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 19.500 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.025 ; 0.800 ; 1255 REMARK 3 BOND ANGLES (DEGREES) : 2.946 ; 1.300 ; 1681 REMARK 3 TORSION ANGLES (DEGREES) : 18.684; 0.000 ; 760 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.012 ; 2.000 ; 40 REMARK 3 GENERAL PLANES (A) : 0.021 ; 5.000 ; 170 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 14.285; 0.000 ; 1247 REMARK 3 NON-BONDED CONTACTS (A) : 0.039 ; 10.000; 35 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : 0 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : MOEWS AND KRETSINGER REMARK 3 KSOL : 0.87 REMARK 3 BSOL : 233.1 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : ISOTROPIC REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NVH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040351. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35259 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 27.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 64.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHARP, EPMR REMARK 200 STARTING MODEL: PDB ENTRY 5I1B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL SOLUTION OF 2.2 - 2.8 M AMMONIUM REMARK 280 SULFATE, 100 MM TRIS, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K, PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 37.67950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 56.51925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.83975 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 SER A 153 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 A 249 O HOH A 288 2.17 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 GLU A 37 CD GLU A 37 OE2 0.088 REMARK 500 GLU A 50 CD GLU A 50 OE2 0.079 REMARK 500 GLU A 105 CD GLU A 105 OE2 0.094 REMARK 500 GLU A 113 CD GLU A 113 OE1 0.084 REMARK 500 GLU A 128 CD GLU A 128 OE1 -0.078 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 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 12 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP A 12 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ASP A 35 CB - CG - OD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 54 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 75 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 86 CB - CG - OD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASN A 129 N - CA - CB ANGL. DEV. = -12.9 DEGREES REMARK 500 ASP A 142 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 142 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES 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 A 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 161 DBREF 2NVH A 1 153 UNP P01584 IL1B_HUMAN 117 269 SEQRES 1 A 153 ALA PRO VAL ARG SER LEU ASN CYS THR LEU ARG ASP SER SEQRES 2 A 153 GLN GLN LYS SER LEU VAL MET SER GLY PRO TYR GLU LEU SEQRES 3 A 153 LYS ALA LEU HIS LEU GLN GLY GLN ASP MET GLU GLN GLN SEQRES 4 A 153 VAL VAL PHE SER MET SER PHE VAL GLN GLY GLU GLU SER SEQRES 5 A 153 ASN ASP LYS ILE PRO VAL ALA LEU GLY LEU LYS GLU LYS SEQRES 6 A 153 ASN LEU TYR LEU SER CYS VAL LEU LYS ASP ASP LYS PRO SEQRES 7 A 153 THR LEU GLN LEU GLU SER VAL ASP PRO LYS ASN TYR PRO SEQRES 8 A 153 LYS LYS LYS MET GLU LYS ARG PHE VAL PHE ASN LYS ILE SEQRES 9 A 153 GLU ILE ASN ASN LYS LEU GLU PHE GLU SER ALA GLN PHE SEQRES 10 A 153 PRO ASN TRP TYR ILE SER THR SER GLN ALA GLU ASN MET SEQRES 11 A 153 PRO VAL PHE LEU GLY GLY THR LYS GLY GLY GLN ASP ILE SEQRES 12 A 153 THR ASP PHE THR MET GLN PHE VAL SER SER HET SO4 A 160 5 HET SO4 A 161 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *149(H2 O) HELIX 1 1 GLN A 32 GLN A 39 5 8 HELIX 2 2 GLU A 96 PHE A 99 5 4 SHEET 1 A 7 SER A 5 ASP A 12 0 SHEET 2 A 7 PHE A 42 PHE A 46 -1 O PHE A 42 N CYS A 8 SHEET 3 A 7 LYS A 55 LEU A 62 -1 O GLY A 61 N SER A 43 SHEET 4 A 7 PHE A 101 ILE A 106 -1 O PHE A 101 N VAL A 58 SHEET 5 A 7 LYS A 109 SER A 114 -1 O GLU A 113 N ASN A 102 SHEET 6 A 7 PHE A 146 PHE A 150 -1 O PHE A 146 N LEU A 110 SHEET 7 A 7 SER A 5 ASP A 12 -1 N ARG A 11 O THR A 147 SHEET 1 B 3 SER A 17 MET A 20 0 SHEET 2 B 3 LEU A 26 LEU A 29 -1 O LEU A 29 N SER A 17 SHEET 3 B 3 MET A 130 PRO A 131 -1 O MET A 130 N ALA A 28 SHEET 1 C 2 LEU A 67 LYS A 74 0 SHEET 2 C 2 LYS A 77 SER A 84 -1 O GLN A 81 N SER A 70 SHEET 1 D 2 TYR A 121 SER A 123 0 SHEET 2 D 2 PHE A 133 GLY A 135 -1 O GLY A 135 N TYR A 121 CISPEP 1 TYR A 90 PRO A 91 0 -4.25 SITE 1 AC1 6 ALA A 1 PRO A 2 VAL A 3 LYS A 92 SITE 2 AC1 6 LYS A 93 HOH A 276 SITE 1 AC2 3 GLU A 96 ARG A 98 HOH A 326 CRYST1 54.506 54.506 75.359 90.00 90.00 90.00 P 43 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 0.018347 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013270 0.00000