HEADER HYDROLASE 10-OCT-01 1K5A TITLE CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN DOUBLE VARIANT I119A/F120A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANGIOGENIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.27.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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, RIBONUCLEASE, VASCULARIZATION EXPDTA X-RAY DIFFRACTION AUTHOR D.D.LEONIDAS,R.SHAPIRO,G.V.SUBBARAO,A.RUSSO,K.R.ACHARYA REVDAT 4 16-AUG-23 1K5A 1 REMARK REVDAT 3 27-OCT-21 1K5A 1 REMARK SEQADV REVDAT 2 24-FEB-09 1K5A 1 VERSN REVDAT 1 20-MAR-02 1K5A 0 JRNL AUTH D.D.LEONIDAS,R.SHAPIRO,G.V.SUBBARAO,A.RUSSO,K.R.ACHARYA JRNL TITL CRYSTALLOGRAPHIC STUDIES ON THE ROLE OF THE C-TERMINAL JRNL TITL 2 SEGMENT OF HUMAN ANGIOGENIN IN DEFINING ENZYMATIC POTENCY. JRNL REF BIOCHEMISTRY V. 41 2552 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 11851402 JRNL DOI 10.1021/BI015768Q REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.D.LEONIDAS,R.SHAPIRO,S.C.ALLEN,G.V.SUBBARAO,K.VELURAJA, 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 DOI 10.1006/JMBI.1998.2378 REMARK 2 REMARK 2 RESOLUTION. 2.33 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) : 2.33 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) (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 5222 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) : 0.193 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 286 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.017 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) : 2.33 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.48 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 560 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 34 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.052 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 937 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.10 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.33 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) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.46 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 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) : 2.740 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.360 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.700 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.340 ; 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1K5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014577. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XENTRONICS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS, X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5235 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08700 REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 32.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: PDN ENTRY 2ANG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM ACTATE, SODIUM CITRATE, PEG REMARK 280 4000, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 44.06000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.58000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.06000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.58000 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 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 A 158 LIES ON A SPECIAL POSITION. 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 GLN A 1 REMARK 465 ASP A 2 REMARK 465 ARG A 121 REMARK 465 ARG A 122 REMARK 465 PRO A 123 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 22 -169.93 -105.68 REMARK 500 ASN A 61 24.80 -145.24 REMARK 500 ARG A 66 -125.55 52.98 REMARK 500 GLU A 67 -71.53 -103.02 REMARK 500 PHE A 100 113.10 -162.11 REMARK 500 ALA A 119 46.43 -101.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ANG RELATED DB: PDB REMARK 900 2ANG IS THE CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN OF THE MET(-1) REMARK 900 FORM. REMARK 900 RELATED ID: 1B1I RELATED DB: PDB REMARK 900 1B1I IS THE CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN. REMARK 900 RELATED ID: 1B1J RELATED DB: PDB REMARK 900 1B1J IS THE CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT H13A. REMARK 900 RELATED ID: 1B1E RELATED DB: PDB REMARK 900 1B1E IS THE CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT K40Q. REMARK 900 RELATED ID: 1K58 RELATED DB: PDB REMARK 900 1K58 IS THE CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT D116H. REMARK 900 RELATED ID: 1K59 RELATED DB: PDB REMARK 900 1K59 IS THE CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT Q117G. REMARK 900 RELATED ID: 1K5B RELATED DB: PDB REMARK 900 1K5B IS THE CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT DES(121- REMARK 900 123). DBREF 1K5A A 1 123 UNP P03950 ANGI_HUMAN 25 147 SEQADV 1K5A ALA A 119 UNP P03950 ILE 143 ENGINEERED MUTATION SEQADV 1K5A ALA A 120 UNP P03950 PHE 144 ENGINEERED MUTATION SEQRES 1 A 123 GLN 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 ALA ALA ARG ARG PRO FORMUL 2 HOH *41(H2 O) HELIX 1 1 ASN A 3 TYR A 14 1 12 HELIX 2 2 ASP A 22 ARG A 33 1 12 HELIX 3 3 ASN A 49 ALA A 55 1 7 HELIX 4 4 ILE A 56 GLU A 58 5 3 HELIX 5 5 GLN A 117 ALA A 120 5 4 SHEET 1 A 3 ILE A 42 ILE A 46 0 SHEET 2 A 3 PHE A 76 LEU A 83 -1 O CYS A 81 N ASN A 43 SHEET 3 A 3 TYR A 94 ARG A 101 -1 O ARG A 101 N PHE A 76 SHEET 1 B 4 GLY A 62 HIS A 65 0 SHEET 2 B 4 LEU A 69 SER A 72 -1 O ILE A 71 N ASN A 63 SHEET 3 B 4 VAL A 104 GLU A 108 -1 O VAL A 105 N ARG A 70 SHEET 4 B 4 LEU A 111 LEU A 115 -1 O VAL A 113 N ALA A 106 SSBOND 1 CYS A 26 CYS A 81 1555 1555 2.03 SSBOND 2 CYS A 39 CYS A 92 1555 1555 2.02 SSBOND 3 CYS A 57 CYS A 107 1555 1555 2.04 CISPEP 1 SER A 37 PRO A 38 0 -0.15 CISPEP 2 PRO A 90 PRO A 91 0 -0.18 CRYST1 88.120 41.160 33.660 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 0.011348 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024295 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029709 0.00000