HEADER HYDROLASE 10-OCT-01 1K5B TITLE CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT DES(121-123) 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 1K5B 1 REMARK REVDAT 3 25-DEC-19 1K5B 1 REMARK SEQADV SEQRES LINK REVDAT 2 24-FEB-09 1K5B 1 VERSN REVDAT 1 20-MAR-02 1K5B 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. 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) (%) : 88.4 REMARK 3 NUMBER OF REFLECTIONS : 9945 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) : 0.206 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 528 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) (%) : 91.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1585 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 85 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 963 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.90 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.26 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 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) : 2.280 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.610 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.750 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.600 ; 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 1K5B 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_1000014578. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-97; NULL REMARK 200 TEMPERATURE (KELVIN) : 293; 293 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; SRS REMARK 200 BEAMLINE : NULL; PX9.5 REMARK 200 X-RAY GENERATOR MODEL : SIEMENS; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 0.8 REMARK 200 MONOCHROMATOR : GRAPHITE; MIRRORS REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : XENTRONICS; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10158 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 (%) : 92.3 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 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 (%) : 90.0 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; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2ANG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, SODIUM POTASSIUM REMARK 280 TARTRATE, PEG 6000, PH 5.2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 43.22500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.20500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.22500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.20500 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: 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 166 O HOH A 167 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 95.67 -53.64 REMARK 500 ASN A 61 27.16 -141.30 REMARK 500 ARG A 66 -147.31 66.80 REMARK 500 ASN A 68 12.02 -164.90 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 121 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: 1K5A RELATED DB: PDB REMARK 900 1K5A IS THE CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT I119A/ REMARK 900 F120A. DBREF 1K5B A 1 120 UNP P03950 ANGI_HUMAN 25 147 SEQADV 1K5B A UNP P03950 ARG 145 DELETION SEQADV 1K5B A UNP P03950 ARG 146 DELETION SEQADV 1K5B A UNP P03950 PRO 147 DELETION SEQRES 1 A 120 PCA ASP ASN SER ARG TYR THR HIS PHE LEU THR GLN HIS SEQRES 2 A 120 TYR ASP ALA LYS PRO GLN GLY ARG ASP ASP ARG TYR CYS SEQRES 3 A 120 GLU SER ILE MET ARG ARG ARG GLY LEU THR SER PRO CYS SEQRES 4 A 120 LYS ASP ILE ASN THR PHE ILE HIS GLY ASN LYS ARG SER SEQRES 5 A 120 ILE LYS ALA ILE CYS GLU ASN LYS ASN GLY ASN PRO HIS SEQRES 6 A 120 ARG GLU ASN LEU ARG ILE SER LYS SER SER PHE GLN VAL SEQRES 7 A 120 THR THR CYS LYS LEU HIS GLY GLY SER PRO TRP PRO PRO SEQRES 8 A 120 CYS GLN TYR ARG ALA THR ALA GLY PHE ARG ASN VAL VAL SEQRES 9 A 120 VAL ALA CYS GLU ASN GLY LEU PRO VAL HIS LEU ASP GLN SEQRES 10 A 120 SER ILE PHE MODRES 1K5B PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 8 HET CIT A 121 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 *57(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 ILE A 56 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 O CYS A 81 N ASN A 43 SHEET 3 A 3 GLN A 93 ARG A 101 -1 O GLN A 93 N HIS A 84 SHEET 1 B 4 GLY A 62 HIS A 65 0 SHEET 2 B 4 LEU A 69 SER A 72 -1 O LEU A 69 N HIS A 65 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 2.01 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 0.09 CISPEP 2 PRO A 90 PRO A 91 0 -0.06 SITE 1 AC1 7 ASP A 41 ASN A 49 ARG A 51 SER A 52 SITE 2 AC1 7 LYS A 82 LEU A 83 ARG A 95 CRYST1 86.450 40.410 32.980 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 0.011567 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030321 0.00000 HETATM 1 N PCA A 1 23.644 16.006 -8.249 1.00 76.74 N HETATM 2 CA PCA A 1 24.316 15.028 -7.367 1.00 76.57 C HETATM 3 CB PCA A 1 25.696 14.765 -7.944 1.00 76.33 C HETATM 4 CG PCA A 1 25.740 15.645 -9.194 1.00 77.07 C HETATM 5 CD PCA A 1 24.414 16.362 -9.273 1.00 76.15 C HETATM 6 OE PCA A 1 24.097 17.158 -10.154 1.00 74.99 O HETATM 7 C PCA A 1 24.372 15.270 -5.852 1.00 76.21 C HETATM 8 O PCA A 1 24.737 16.344 -5.356 1.00 75.15 O