PDB Short entry for 2QCA HEADER HYDROLASE 19-JUN-07 2QCA TITLE A NEW CRYSTAL FORM OF BOVINE PANCREATIC RNASE A IN COMPLEX WITH 2'- TITLE 2 DEOXYGUANOSINE-5'-MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE PANCREATIC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE 1, RNASE A; COMPND 5 EC: 3.1.27.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 TISSUE: PANCREAS KEYWDS RIBONUCLEASE, PROTEIN-NUCLEOTIDE COMPLEX, STRUCTURAL GENOMICS, PSI-2, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, CENTER FOR HIGH-THROUGHPUT STRUCTURAL KEYWDS 3 BIOLOGY, CHTSB, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.B.LARSON,J.S.DAY,R.CUDNEY,A.MCPHERSON,CENTER FOR HIGH-THROUGHPUT AUTHOR 2 STRUCTURAL BIOLOGY (CHTSB) REVDAT 6 30-AUG-23 2QCA 1 REMARK REVDAT 5 13-JUL-11 2QCA 1 VERSN REVDAT 4 24-FEB-09 2QCA 1 VERSN REVDAT 3 11-SEP-07 2QCA 1 JRNL REVDAT 2 17-JUL-07 2QCA 1 REMARK REVDAT 1 03-JUL-07 2QCA 0 JRNL AUTH S.B.LARSON,J.S.DAY,R.CUDNEY,A.MCPHERSON JRNL TITL A NEW CRYSTAL FORM OF BOVINE PANCREATIC RNASE A IN COMPLEX JRNL TITL 2 WITH 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 63 728 2007 JRNL REFN ESSN 1744-3091 JRNL PMID 17768339 JRNL DOI 10.1107/S1744309107039565 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.B.LARSON,J.S.DAY,R.CUDNEY,A.MCPHERSON REMARK 1 TITL A NOVEL STRATEGY FOR THE CRYSTALLIZATION OF PROTEINS: X-RAY REMARK 1 TITL 2 DIFFRACTION VALIDATION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. D63 310 2007 REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 1.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.4 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.125 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.119 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 11.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2672 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 26810 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.115 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.110 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.800 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1797 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 16646 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 951 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1105.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 914.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 12 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10604 REMARK 3 NUMBER OF RESTRAINTS : 13217 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.065 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.073 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.020 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.067 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.091 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: DGP FROM PARKINSON, ET AL., ACTA CRYST. REMARK 3 D52(1996)57-64 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGEN ATOMS WERE INCLUDED IN RIDING REMARK 3 POSITIONS. HYDROGEN ATOMS OF HYDROXYL GROUPS WERE PLACED BY HAND REMARK 3 BASED ON BEST HYDROGEN BONDING INTERACTIONS. WATER MOLECULES REMARK 3 WERE OBTAINED INITIALLY FOUND FROM AUTOMATIC MAP INTERPRETATION REMARK 3 AND LATER FROM MANUAL IDENTIFICATION FROM FO-FC AND 2FO-FC MAPS. REMARK 3 WATER OCCUPANCIES WERE INITIALLY SET TO 1.0, BUT REDUCED TO 0.5 REMARK 3 IF B VALUES EXCEEDED 80 A^2. REMARK 4 REMARK 4 2QCA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043418. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-06 REMARK 200 TEMPERATURE (KELVIN) : 295.0 REMARK 200 PH : 7.00 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 : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27155 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 27.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : 3.330 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 24.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.49 REMARK 200 R MERGE FOR SHELL (I) : 0.49100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1RNO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR: 0.6 ML OF 30% PEG 3350 IN REMARK 280 0.1 M HEPES AT PH 7.0. SAMPLE: 2 UL 10-40 MG/ML PROTEIN IN 0.1 M REMARK 280 HEPES AT PH 7.0 AND 2 UL OF 0.1 M DGP, CHOLESTEROL, THYMINE AND REMARK 280 OXAMIC ACID IN 15% PEG 3350 AND 9.1 M HEPES AT PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K, PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.06667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.13333 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: 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 TYR A 73 CG - CD1 - CE1 ANGL. DEV. = 5.5 DEGREES 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 ASN A 34 35.91 71.07 REMARK 500 HIS A 48 61.01 -104.10 REMARK 500 GLN A 60 -131.94 -104.83 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 DGP A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGP A 300 DBREF 2QCA A 1 124 UNP P61823 RNAS1_BOVIN 27 150 SEQRES 1 A 124 LYS GLU THR ALA ALA ALA LYS PHE GLU ARG GLN HIS MET SEQRES 2 A 124 ASP SER SER THR SER ALA ALA SER SER SER ASN TYR CYS SEQRES 3 A 124 ASN GLN MET MET LYS SER ARG ASN LEU THR LYS ASP ARG SEQRES 4 A 124 CYS LYS PRO VAL ASN THR PHE VAL HIS GLU SER LEU ALA SEQRES 5 A 124 ASP VAL GLN ALA VAL CYS SER GLN LYS ASN VAL ALA CYS SEQRES 6 A 124 LYS ASN GLY GLN THR ASN CYS TYR GLN SER TYR SER THR SEQRES 7 A 124 MET SER ILE THR ASP CYS ARG GLU THR GLY SER SER LYS SEQRES 8 A 124 TYR PRO ASN CYS ALA TYR LYS THR THR GLN ALA ASN LYS SEQRES 9 A 124 HIS ILE ILE VAL ALA CYS GLU GLY ASN PRO TYR VAL PRO SEQRES 10 A 124 VAL HIS PHE ASP ALA SER VAL HET DGP A 200 23 HET DGP A 300 23 HETNAM DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE FORMUL 2 DGP 2(C10 H14 N5 O7 P) FORMUL 4 HOH *137(H2 O) HELIX 1 1 THR A 3 MET A 13 1 11 HELIX 2 2 ASN A 24 ARG A 33 1 10 HELIX 3 3 SER A 50 ALA A 56 1 7 HELIX 4 4 VAL A 57 GLN A 60 5 4 SHEET 1 A 3 VAL A 43 VAL A 47 0 SHEET 2 A 3 MET A 79 GLU A 86 -1 O THR A 82 N PHE A 46 SHEET 3 A 3 TYR A 97 LYS A 104 -1 O THR A 100 N ASP A 83 SHEET 1 B 4 LYS A 61 VAL A 63 0 SHEET 2 B 4 CYS A 72 GLN A 74 -1 O GLN A 74 N LYS A 61 SHEET 3 B 4 ILE A 106 GLU A 111 -1 O VAL A 108 N TYR A 73 SHEET 4 B 4 VAL A 116 SER A 123 -1 O VAL A 118 N ALA A 109 SSBOND 1 CYS A 26 CYS A 84 1555 1555 2.02 SSBOND 2 CYS A 40 CYS A 95 1555 1555 2.04 SSBOND 3 CYS A 58 CYS A 110 1555 1555 2.02 SSBOND 4 CYS A 65 CYS A 72 1555 1555 1.98 CISPEP 1 TYR A 92 PRO A 93 0 -2.95 CISPEP 2 ASN A 113 PRO A 114 0 8.07 SITE 1 AC1 17 HIS A 12 SER A 22 ASN A 24 GLN A 28 SITE 2 AC1 17 VAL A 43 ASN A 44 THR A 45 LYS A 66 SITE 3 AC1 17 ARG A 85 PHE A 120 ASP A 121 DGP A 300 SITE 4 AC1 17 HOH A 477 HOH A 484 HOH A 521 HOH A 522 SITE 5 AC1 17 HOH A 523 SITE 1 AC2 22 LYS A 7 GLN A 11 HIS A 12 LYS A 41 SITE 2 AC2 22 CYS A 58 SER A 59 GLN A 69 TYR A 73 SITE 3 AC2 22 GLU A 111 TYR A 115 VAL A 118 HIS A 119 SITE 4 AC2 22 PHE A 120 DGP A 200 HOH A 409 HOH A 454 SITE 5 AC2 22 HOH A 455 HOH A 475 HOH A 480 HOH A 481 SITE 6 AC2 22 HOH A 482 HOH A 483 CRYST1 55.080 55.080 39.200 90.00 90.00 120.00 P 31 3 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 0.018155 0.010482 0.000000 0.00000 SCALE2 0.000000 0.020964 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025510 0.00000