3D5G - Header Asymmetric Unit

HEADER HYDROLASE 16-MAY-08 3D5G

TITLE STRUCTURE OF RIBONUCLEASE SA2 COMPLEXES WITH TITLE 2 MONONUCLEOTIDES: NEW ASPECTS OF CATALYTIC REACTION AND TITLE 3 SUBSTRATE RECOGNITION

COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: RIBONUCLEASE SA2; COMPND 5 EC: 3.1.4.8; COMPND 6 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES AUREOFACIENS; SOURCE 3 ORGANISM_TAXID: 1894; SOURCE 4 STRAIN: R8/26; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: NOVABLUE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PEH200

KEYWDS RIBONUCLEASE, HYDROLASE

EXPDTA X-RAY DIFFRACTION

AUTHOR V.BAUEROVA-HLINKOVA,R.DVORSKY,F.POVAZANEC,J.SEVCIK

REVDAT 2 04-AUG-09 3D5G 1 JRNL REVDAT 1 26-MAY-09 3D5G 0

JRNL AUTH V.BAUEROVA-HLINKOVA,R.DVORSKY,D.PERECKO, JRNL AUTH 2 F.POVAZANEC,J.SEVCIK JRNL TITL STRUCTURE OF RNASE SA2 COMPLEXES WITH JRNL TITL 2 MONONUCLEOTIDES - NEW ASPECTS OF CATALYTIC REACTION JRNL TITL 3 AND SUBSTRATE RECOGNITION JRNL REF FEBS J. V. 276 4156 2009 JRNL REFN ISSN 1742-464X JRNL PMID 19558492 JRNL DOI 10.1111/J.1742-4658.2009.07125.X

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 32393 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 + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1713 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1956 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.1660 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.2500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2307 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 505 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45000 REMARK 3 B22 (A**2) : 1.46000 REMARK 3 B33 (A**2) : -0.92000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.25000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.203 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.780 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2377 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1648 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3238 ; 1.892 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3959 ; 1.554 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 286 ; 7.176 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;33.464 ;23.203 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 354 ;16.117 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;19.485 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 325 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2715 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 514 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 637 ; 0.231 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1922 ; 0.231 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1136 ; 0.192 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1287 ; 0.092 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 391 ; 0.244 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.307 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 13 ; 0.309 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 55 ; 0.255 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 51 ; 0.259 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1783 ; 2.203 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 578 ; 0.777 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2331 ; 2.739 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1114 ; 3.684 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 907 ; 4.954 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4959 ; 2.618 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 505 ; 9.982 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3960 ; 4.315 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS

REMARK 4 REMARK 4 3D5G COMPLIES WITH FORMAT V. 3.20, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-MAY-08. REMARK 100 THE RCSB ID CODE IS RCSB047615.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : MONOCHROMATOR SI (111) REMARK 200 OPTICS : NULL 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 : 34199 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 12.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.1600 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) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: 1PYL REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% AMMONIUM SULPHATE, PH 7.2, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 50.32750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.83350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.32750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.83350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL

REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 168 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 197 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 ALA A 1 REMARK 465 ALA C 1

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 157 O HOH A 483 1.85 REMARK 500 O HOH C 292 O HOH C 482 1.99 REMARK 500 O HOH B 128 O HOH B 493 2.01 REMARK 500 O HOH A 157 O HOH A 488 2.02 REMARK 500 O HOH C 415 O HOH C 459 2.08 REMARK 500 OD1 ASN B 27 O HOH B 485 2.11 REMARK 500 OD1 ASP B 2 O HOH B 484 2.12 REMARK 500 O HOH C 317 O HOH C 480 2.13 REMARK 500 O HOH B 201 O HOH B 481 2.14 REMARK 500 N LEU A 5 O HOH A 211 2.16 REMARK 500 NZ LYS B 26 O GLY B 28 2.18 REMARK 500 O HOH B 448 O HOH B 474 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 111 O HOH B 486 4555 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 70 CD ARG A 70 NE -0.118 REMARK 500 GLU C 40 CB GLU C 40 CG 0.119 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 70 NE - CZ - NH2 ANGL. DEV. = -9.1 DEGREES REMARK 500 ASP A 85 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASN C 33 O - C - N ANGL. DEV. = -11.6 DEGREES REMARK 500 ARG C 34 C - N - CA ANGL. DEV. = -24.3 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 SER A 64 -154.71 -157.52 REMARK 500 SER B 64 150.71 -46.01 REMARK 500 PRO C 3 137.36 -35.30 REMARK 500 ALA C 4 -179.56 -64.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ARG C 34 21.4 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL

REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 108 DISTANCE = 8.21 ANGSTROMS REMARK 525 HOH B 128 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH A 111 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A 116 DISTANCE = 8.12 ANGSTROMS REMARK 525 HOH A 144 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH A 145 DISTANCE = 8.34 ANGSTROMS REMARK 525 HOH A 150 DISTANCE = 9.01 ANGSTROMS REMARK 525 HOH A 152 DISTANCE = 10.49 ANGSTROMS REMARK 525 HOH B 272 DISTANCE = 9.52 ANGSTROMS REMARK 525 HOH B 275 DISTANCE = 9.17 ANGSTROMS REMARK 525 HOH B 281 DISTANCE = 8.50 ANGSTROMS REMARK 525 HOH B 282 DISTANCE = 8.01 ANGSTROMS REMARK 525 HOH C 418 DISTANCE = 10.22 ANGSTROMS REMARK 525 HOH B 438 DISTANCE = 9.64 ANGSTROMS REMARK 525 HOH B 486 DISTANCE = 5.46 ANGSTROMS REMARK 525 HOH B 493 DISTANCE = 5.25 ANGSTROMS REMARK 525 HOH C 464 DISTANCE = 5.33 ANGSTROMS REMARK 525 HOH C 487 DISTANCE = 5.44 ANGSTROMS

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 98

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PYL RELATED DB: PDB REMARK 900 RELATED ID: 1PY3 RELATED DB: PDB REMARK 900 RELATED ID: 3D4A RELATED DB: PDB REMARK 900 RELATED ID: 3D5I RELATED DB: PDB

DBREF 3D5G A 1 97 UNP Q53752 Q53752_STRAU 67 163 DBREF 3D5G B 1 97 UNP Q53752 Q53752_STRAU 67 163 DBREF 3D5G C 1 97 UNP Q53752 Q53752_STRAU 67 163

SEQRES 1 A 97 ALA ASP PRO ALA LEU ALA ASP VAL CYS ARG THR LYS LEU SEQRES 2 A 97 PRO SER GLN ALA GLN ASP THR LEU ALA LEU ILE ALA LYS SEQRES 3 A 97 ASN GLY PRO TYR PRO TYR ASN ARG ASP GLY VAL VAL PHE SEQRES 4 A 97 GLU ASN ARG GLU SER ARG LEU PRO LYS LYS GLY ASN GLY SEQRES 5 A 97 TYR TYR HIS GLU PHE THR VAL VAL THR PRO GLY SER ASN SEQRES 6 A 97 ASP ARG GLY THR ARG ARG VAL VAL THR GLY GLY TYR GLY SEQRES 7 A 97 GLU GLN TYR TRP SER PRO ASP HIS TYR ALA THR PHE GLN SEQRES 8 A 97 GLU ILE ASP PRO ARG CYS SEQRES 1 B 97 ALA ASP PRO ALA LEU ALA ASP VAL CYS ARG THR LYS LEU SEQRES 2 B 97 PRO SER GLN ALA GLN ASP THR LEU ALA LEU ILE ALA LYS SEQRES 3 B 97 ASN GLY PRO TYR PRO TYR ASN ARG ASP GLY VAL VAL PHE SEQRES 4 B 97 GLU ASN ARG GLU SER ARG LEU PRO LYS LYS GLY ASN GLY SEQRES 5 B 97 TYR TYR HIS GLU PHE THR VAL VAL THR PRO GLY SER ASN SEQRES 6 B 97 ASP ARG GLY THR ARG ARG VAL VAL THR GLY GLY TYR GLY SEQRES 7 B 97 GLU GLN TYR TRP SER PRO ASP HIS TYR ALA THR PHE GLN SEQRES 8 B 97 GLU ILE ASP PRO ARG CYS SEQRES 1 C 97 ALA ASP PRO ALA LEU ALA ASP VAL CYS ARG THR LYS LEU SEQRES 2 C 97 PRO SER GLN ALA GLN ASP THR LEU ALA LEU ILE ALA LYS SEQRES 3 C 97 ASN GLY PRO TYR PRO TYR ASN ARG ASP GLY VAL VAL PHE SEQRES 4 C 97 GLU ASN ARG GLU SER ARG LEU PRO LYS LYS GLY ASN GLY SEQRES 5 C 97 TYR TYR HIS GLU PHE THR VAL VAL THR PRO GLY SER ASN SEQRES 6 C 97 ASP ARG GLY THR ARG ARG VAL VAL THR GLY GLY TYR GLY SEQRES 7 C 97 GLU GLN TYR TRP SER PRO ASP HIS TYR ALA THR PHE GLN SEQRES 8 C 97 GLU ILE ASP PRO ARG CYS

HET SO4 A 98 5

HETNAM SO4 SULFATE ION

FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *505(H2 O)

HELIX 1 1 THR A 11 LEU A 13 5 3 HELIX 2 2 PRO A 14 LYS A 26 1 13 HELIX 3 3 THR B 11 LEU B 13 5 3 HELIX 4 4 PRO B 14 LYS B 26 1 13 HELIX 5 5 THR C 11 LEU C 13 5 3 HELIX 6 6 PRO C 14 LYS C 26 1 13

SHEET 1 A 6 ALA A 6 CYS A 9 0 SHEET 2 A 6 GLN A 91 ASP A 94 1 O GLU A 92 N ALA A 6 SHEET 3 A 6 GLN A 80 SER A 83 -1 N TRP A 82 O GLN A 91 SHEET 4 A 6 ARG A 71 THR A 74 -1 N ARG A 71 O SER A 83 SHEET 5 A 6 TYR A 54 THR A 58 -1 N HIS A 55 O THR A 74 SHEET 6 A 6 VAL A 38 PHE A 39 -1 N PHE A 39 O TYR A 54 SHEET 1 B 5 ALA B 6 CYS B 9 0 SHEET 2 B 5 GLN B 91 ASP B 94 1 O ASP B 94 N VAL B 8 SHEET 3 B 5 GLN B 80 SER B 83 -1 N TRP B 82 O GLN B 91 SHEET 4 B 5 ARG B 71 THR B 74 -1 N VAL B 73 O TYR B 81 SHEET 5 B 5 HIS B 55 THR B 58 -1 N PHE B 57 O VAL B 72 SHEET 1 C 6 ASP C 7 CYS C 9 0 SHEET 2 C 6 GLN C 91 ASP C 94 1 O ASP C 94 N VAL C 8 SHEET 3 C 6 GLN C 80 SER C 83 -1 N GLN C 80 O ILE C 93 SHEET 4 C 6 ARG C 71 THR C 74 -1 N VAL C 73 O TYR C 81 SHEET 5 C 6 TYR C 54 THR C 58 -1 N HIS C 55 O THR C 74 SHEET 6 C 6 VAL C 37 PHE C 39 -1 N PHE C 39 O TYR C 54

SSBOND 1 CYS A 9 CYS A 97 1555 1555 2.00 SSBOND 2 CYS B 9 CYS B 97 1555 1555 2.04 SSBOND 3 CYS C 9 CYS C 97 1555 1555 2.02

CISPEP 1 GLY A 28 PRO A 29 0 -6.00 CISPEP 2 GLY B 28 PRO B 29 0 15.61 CISPEP 3 GLY C 28 PRO C 29 0 2.67

SITE 1 AC1 8 ARG A 34 GLU A 56 ARG A 67 ARG A 71 SITE 2 AC1 8 HIS A 86 TYR A 87 HOH A 199 ARG C 45

CRYST1 100.655 67.667 57.085 90.00 100.63 90.00 C 1 2 1 12

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 0.009935 0.000000 0.001865 0.00000

SCALE2 0.000000 0.014778 0.000000 0.00000

SCALE3 0.000000 0.000000 0.017824 0.00000