HEADER HYDROLASE 20-NOV-98 1B1I TITLE CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROLASE 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 HYDROLASE (VASCULARIZATION), HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.D.LEONIDAS,K.R.ACHARYA REVDAT 7 09-OCT-24 1B1I 1 REMARK REVDAT 6 09-AUG-23 1B1I 1 REMARK REVDAT 5 25-DEC-19 1B1I 1 SEQADV SEQRES LINK REVDAT 4 24-FEB-09 1B1I 1 VERSN REVDAT 3 01-APR-03 1B1I 1 JRNL REVDAT 2 20-MAR-00 1B1I 1 REMARK REVDAT 1 02-APR-99 1B1I 0 JRNL AUTH D.D.LEONIDAS,R.SHAPIRO,S.C.ALLEN,G.V.SUBBARAO,K.VELURAJA, JRNL AUTH 2 K.R.ACHARYA JRNL TITL REFINED CRYSTAL STRUCTURES OF NATIVE HUMAN ANGIOGENIN AND JRNL TITL 2 TWO ACTIVE SITE VARIANTS: IMPLICATIONS FOR THE UNIQUE JRNL TITL 3 FUNCTIONAL PROPERTIES OF AN ENZYME INVOLVED IN JRNL TITL 4 NEOVASCULARISATION DURING TUMOUR GROWTH. JRNL REF J.MOL.BIOL. V. 285 1209 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 9918722 JRNL DOI 10.1006/JMBI.1998.2378 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 86.1 REMARK 3 NUMBER OF REFLECTIONS : 11348 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) : 0.222 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 550 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 52.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1055 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 63 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 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 : 13 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.60 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.30 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) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.880 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) : 2.270 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.790 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.550 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.740 ; 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 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1B1I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-NOV-98. REMARK 100 THE DEPOSITION ID IS D_1000000126. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 289 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 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 : 11357 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.37800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 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 1ANG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.6 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 42.32500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.90500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.32500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.90500 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 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 -42.65 164.40 REMARK 500 ASN A 3 108.83 39.91 REMARK 500 GLN A 19 -90.76 -104.63 REMARK 500 ARG A 21 61.52 -110.07 REMARK 500 SER A 37 86.24 -151.09 REMARK 500 ASN A 61 25.23 -155.13 REMARK 500 ARG A 66 -145.15 53.70 REMARK 500 ARG A 122 71.04 -114.56 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 CIT A 1054 DBREF 1B1I A 1 123 UNP P03950 ANGI_HUMAN 1 123 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 1B1I PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 8 HET CIT A1054 13 HETNAM PCA PYROGLUTAMIC ACID HETNAM CIT CITRIC ACID FORMUL 1 PCA C5 H7 N O3 FORMUL 2 CIT C6 H8 O7 FORMUL 3 HOH *53(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 A 3 ILE A 42 ILE A 46 0 SHEET 2 A 3 PHE A 76 HIS A 84 -1 N CYS A 81 O ASN A 43 SHEET 3 A 3 GLN A 93 ARG A 101 -1 N ARG A 101 O PHE A 76 SHEET 1 B 2 GLY A 62 HIS A 65 0 SHEET 2 B 2 LEU A 69 SER A 72 -1 N ILE A 71 O ASN A 63 SHEET 1 C 2 VAL A 105 GLU A 108 0 SHEET 2 C 2 LEU A 111 LEU A 115 -1 N HIS A 114 O ALA A 106 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 2.03 LINK C PCA A 1 N ASP A 2 1555 1555 1.34 CISPEP 1 SER A 37 PRO A 38 0 0.08 CISPEP 2 PRO A 90 PRO A 91 0 0.12 SITE 1 AC1 8 HIS A 65 ILE A 71 GLY A 99 PHE A 100 SITE 2 AC1 8 ARG A 101 ILE A 119 HOH A1014 HOH A1017 CRYST1 84.650 37.810 42.390 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 0.011813 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026448 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023590 0.00000 HETATM 1 N PCA A 1 28.375 13.851 -2.979 1.00 68.90 N HETATM 2 CA PCA A 1 27.259 12.924 -3.303 1.00 68.92 C HETATM 3 CB PCA A 1 27.421 12.492 -4.761 1.00 67.18 C HETATM 4 CG PCA A 1 28.685 13.243 -5.215 1.00 67.68 C HETATM 5 CD PCA A 1 29.182 14.049 -4.021 1.00 68.25 C HETATM 6 OE PCA A 1 30.185 14.775 -4.024 1.00 65.62 O HETATM 7 C PCA A 1 26.977 11.731 -2.378 1.00 68.14 C HETATM 8 O PCA A 1 27.213 10.566 -2.727 1.00 66.93 O