HEADER ANGIOGENIN 21-APR-01 1HBY TITLE BINDING OF PHOSPHATE AND PYROPHOSPHATE IONS AT THE ACTIVE SITE OF TITLE 2 HUMAN ANGIOGENIN AS REVEALED BY X-RAY CRYSTALLOGRAPHY COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANGIOGENIN; COMPND 3 CHAIN: A; COMPND 4 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 KEYWDS ANGIOGENIN, RIBONUCLEASE, PHOSPHATE, PYROPHOSPHATE EXPDTA X-RAY DIFFRACTION AUTHOR D.D.LEONIDAS,G.B.CHAVALI,A.S.JARDINE,S.LI,R.SHAPIRO,K.R.ACHARYA REVDAT 5 20-NOV-24 1HBY 1 REMARK REVDAT 4 13-DEC-23 1HBY 1 REMARK REVDAT 3 11-MAR-20 1HBY 1 SEQRES LINK REVDAT 2 24-FEB-09 1HBY 1 VERSN REVDAT 1 09-AUG-01 1HBY 0 JRNL AUTH D.D.LEONIDAS,G.B.CHAVALI,A.M.JARDINE,S.LI,R.SHAPIRO, JRNL AUTH 2 K.R.ACHARYA JRNL TITL BINDING OF PHOSPHATE AND PYROPHOSPHATE IONS AT THE ACTIVE JRNL TITL 2 SITE OF HUMAN ANGIOGENIN AS REVEALED BY X-RAY JRNL TITL 3 CRYSTALLOGRAPHY JRNL REF PROTEIN SCI. V. 10 1669 2001 JRNL REFN ISSN 0961-8368 JRNL PMID 11468363 JRNL DOI 10.1110/PS.13601 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.D.LEONIDAS,R.SHAPIRO,S.C.ALLEN,G.V.SUBBARAO,K.VELOURAJA, REMARK 1 AUTH 2 K.R.ACHARYA REMARK 1 TITL REFINED CRYSTAL STRUCTURES OF NATIVE HUMAN ANGIOGENIN AND REMARK 1 TITL 2 TWO ACTIVE SITE VARIANTS: IMPLICATIONS FOR THE UNIQUE REMARK 1 TITL 3 FUNCTIONAL PROPERTIES OF AN ENZYME INVOLVED IN REMARK 1 TITL 4 NEOVASCULARISATION DURING TUMOUR GROWTH REMARK 1 REF J.MOL.BIOL. V. 285 1209 1999 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 9918722 REMARK 1 DOI 10.1006/JMBI.1998.2378 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 7447 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 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.600 REMARK 3 FREE R VALUE TEST SET COUNT : 566 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1181 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 83 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 992 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 46 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.770 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.670 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.660 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.020 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PARAM.WATER REMARK 3 PARAMETER FILE 3 : PO4.PARAM REMARK 3 PARAMETER FILE 4 : PCA.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPOW.WATER REMARK 3 TOPOLOGY FILE 3 : PO4.TOP REMARK 3 TOPOLOGY FILE 4 : PCA.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1HBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-APR-01. REMARK 100 THE DEPOSITION ID IS D_1290008005. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-98 REMARK 200 TEMPERATURE (KELVIN) : 287.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7458 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.15200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 11.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1B1I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 6000, 0.1M MES, PH 6.0, 0.1M REMARK 280 NACL, PH 6.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 43.10300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.20250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.10300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.20250 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2024 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 TRNA-SPECIFIC RIBONUCLEASE THAT BINDS TO ACTIN ON THE REMARK 400 SURFACE OF ENDOTHELIAL CELLS 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 ASP A 2 -130.12 35.12 REMARK 500 GLN A 19 -157.07 76.54 REMARK 500 ARG A 21 50.31 -105.68 REMARK 500 SER A 37 84.49 -152.12 REMARK 500 ASN A 61 18.71 -140.47 REMARK 500 ARG A 66 -136.61 49.46 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 PO4 A1124 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A4Y RELATED DB: PDB REMARK 900 RIBONUCLEASE INHIBITOR-ANGIOGENIN COMPLEX REMARK 900 RELATED ID: 1ANG RELATED DB: PDB REMARK 900 ANGIOGENIN REMARK 900 RELATED ID: 1AWZ RELATED DB: PDB REMARK 900 3D SOLUTION STRUCTURE OF HUMAN ANGIOGENIN DETERMINED BY 1H, 15N NMR REMARK 900 SPECTROSCOPY, 30 STRUCTURES REMARK 900 RELATED ID: 1B1E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT K40Q REMARK 900 RELATED ID: 1B1I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN REMARK 900 RELATED ID: 1B1J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT H13A. REMARK 900 RELATED ID: 2ANG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN OF THE MET(-1) FORM DBREF 1HBY A 1 123 UNP P03950 ANGI_HUMAN 25 147 SEQADV 1HBY PCA A 1 UNP P03950 GLU 25 MODIFIED RESIDUE SEQRES 1 A 123 PCA ASP ASN SER ARG TYR THR HIS PHE LEU THR GLN HIS SEQRES 2 A 123 TYR ASP ALA LYS PRO GLN GLY ARG ASP ASP ARG TYR CYS SEQRES 3 A 123 GLU SER ILE MET ARG ARG ARG GLY LEU THR SER PRO CYS SEQRES 4 A 123 LYS ASP ILE ASN THR PHE ILE HIS GLY ASN LYS ARG SER SEQRES 5 A 123 ILE LYS ALA ILE CYS GLU ASN LYS ASN GLY ASN PRO HIS SEQRES 6 A 123 ARG GLU ASN LEU ARG ILE SER LYS SER SER PHE GLN VAL SEQRES 7 A 123 THR THR CYS LYS LEU HIS GLY GLY SER PRO TRP PRO PRO SEQRES 8 A 123 CYS GLN TYR ARG ALA THR ALA GLY PHE ARG ASN VAL VAL SEQRES 9 A 123 VAL ALA CYS GLU ASN GLY LEU PRO VAL HIS LEU ASP GLN SEQRES 10 A 123 SER ILE PHE ARG ARG PRO MODRES 1HBY PCA A 1 GLU PYROGLUTAMIC ACID HET PCA A 1 8 HET PO4 A1124 5 HETNAM PCA PYROGLUTAMIC ACID HETNAM PO4 PHOSPHATE ION FORMUL 1 PCA C5 H7 N O3 FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *46(H2 O) HELIX 1 1 SER A 4 HIS A 13 1 10 HELIX 2 2 ASP A 23 ARG A 32 1 10 HELIX 3 3 LYS A 50 CYS A 57 1 8 HELIX 4 4 GLN A 117 PHE A 120 5 4 SHEET 1 AA 3 ILE A 42 ILE A 46 0 SHEET 2 AA 3 PHE A 76 HIS A 84 -1 O THR A 79 N PHE A 45 SHEET 3 AA 3 GLN A 93 ARG A 101 -1 O GLN A 93 N HIS A 84 SHEET 1 AB 4 GLY A 62 HIS A 65 0 SHEET 2 AB 4 LEU A 69 SER A 72 -1 O LEU A 69 N HIS A 65 SHEET 3 AB 4 VAL A 104 GLU A 108 -1 O VAL A 105 N ARG A 70 SHEET 4 AB 4 LEU A 111 LEU A 115 -1 O LEU A 111 N GLU A 108 SSBOND 1 CYS A 26 CYS A 81 1555 1555 2.04 SSBOND 2 CYS A 39 CYS A 92 1555 1555 2.01 SSBOND 3 CYS A 57 CYS A 107 1555 1555 2.02 LINK C PCA A 1 N ASP A 2 1555 1555 1.33 CISPEP 1 SER A 37 PRO A 38 0 0.14 CISPEP 2 PRO A 90 PRO A 91 0 -0.30 SITE 1 AC1 5 GLN A 12 HIS A 13 LYS A 40 HIS A 114 SITE 2 AC1 5 LEU A 115 CRYST1 86.206 38.405 33.568 90.00 90.00 90.00 P 21 21 2 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 0.011600 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026038 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029790 0.00000 HETATM 1 N PCA A 1 12.635 15.723 13.187 1.00 76.47 N HETATM 2 CA PCA A 1 12.592 16.451 14.481 1.00 77.05 C HETATM 3 CB PCA A 1 11.140 16.462 14.943 1.00 77.34 C HETATM 4 CG PCA A 1 10.395 15.702 13.830 1.00 76.52 C HETATM 5 CD PCA A 1 11.433 15.297 12.806 1.00 75.17 C HETATM 6 OE PCA A 1 11.190 14.670 11.776 1.00 72.32 O HETATM 7 C PCA A 1 13.466 15.688 15.497 1.00 76.27 C HETATM 8 O PCA A 1 14.597 15.276 15.185 1.00 78.12 O