HEADER HYDROLASE 25-MAY-10 3N5F TITLE CRYSTAL STRUCTURE OF L-N-CARBAMOYLASE FROM GEOBACILLUS TITLE 2 STEAROTHERMOPHILUS CECT43 COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-CARBAMOYL-L-AMINO ACID HYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: L-CARBAMOYLASE; COMPND 5 EC: 3.5.1.87; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_COMMON: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 4 ORGANISM_TAXID: 1422; SOURCE 5 STRAIN: CECT43; SOURCE 6 GENE: AMAB; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET22 KEYWDS CARBAMOYLASE, HINGE DOMAIN, M20 PEPTIDASE FAMILY, EVOLUTION, BINDING KEYWDS 2 RESIDUE, DIMERIZATION DOMAIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.GARCIA-PINO,S.MARTINEZ-RODRIGUEZ,J.A.GAVIRA REVDAT 3 14-NOV-12 3N5F 1 JRNL REVDAT 2 31-OCT-12 3N5F 1 JRNL VERSN REVDAT 1 25-MAY-11 3N5F 0 JRNL AUTH S.MARTINEZ-RODRIGUEZ,A.GARCIA-PINO,F.J.LAS HERAS-VAZQUEZ, JRNL AUTH 2 J.M.CLEMENTE-JIMENEZ,F.RODRIGUEZ-VICO,J.M.GARCIA-RUIZ, JRNL AUTH 3 R.LORIS,J.A.GAVIRA JRNL TITL MUTATIONAL AND STRUCTURAL ANALYSIS OF L-N-CARBAMOYLASE JRNL TITL 2 REVEALS NEW INSIGHTS INTO A PEPTIDASE M20/M25/M40 FAMILY JRNL TITL 3 MEMBER. JRNL REF J.BACTERIOL. V. 194 5759 2012 JRNL REFN ISSN 0021-9193 JRNL PMID 22904279 JRNL DOI 10.1128/JB.01056-12 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.MARTINEZ-RODRIGUEZ,A.GARCIA-PINO,F.J.LAS HERAS-VAZQUEZ, REMARK 1 AUTH 2 J.M.CLEMENTE-JIMENEZ,F.RODRIGUEZ-VICO,R.LORIS, REMARK 1 AUTH 3 J.M.GARCIA-RUIZ,J.A.GAVIRA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC STUDIES OF REMARK 1 TITL 2 THE RECOMBINANT L-N-CARBAMOYLASE FROM GEOBACILLUS REMARK 1 TITL 3 STEAROTHERMOPHILUS CECT43. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 64 1135 2008 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 19052368 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 23771 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1271 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) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1495 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5993 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.82000 REMARK 3 B22 (A**2) : -0.26000 REMARK 3 B33 (A**2) : -1.56000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.396 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.283 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.946 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.811 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6201 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8450 ; 1.556 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 829 ; 6.284 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 243 ;34.850 ;23.457 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 979 ;19.071 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;21.874 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 972 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4704 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 4051 ; 0.604 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6485 ; 1.075 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2150 ; 1.581 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1956 ; 2.695 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.40 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3N5F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUN-10. REMARK 100 THE RCSB ID CODE IS RCSB059402. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.5 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MONTEL OPTICS REMARK 200 OPTICS : KAPPA CONFIGURATION REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25512 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 73.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 7.260 REMARK 200 R MERGE (I) : 0.12380 REMARK 200 R SYM (I) : 0.12380 REMARK 200 FOR THE DATA SET : 15.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.92 REMARK 200 R MERGE FOR SHELL (I) : 0.25780 REMARK 200 R SYM FOR SHELL (I) : 0.25780 REMARK 200 FOR SHELL : 4.160 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: PDB ENTRY 1Z2L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 % ISO-PROPANOL, 0.1 M SODIUM REMARK 280 CACODYLATE PH 6.5 AND 0.6 M TRISODIUM CITRATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 51.60400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 105.84150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.60400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 105.84150 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 MET A 1 REMARK 465 ILE A 2 REMARK 465 MET B 1 REMARK 465 ILE B 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 9 CG CD OE1 NE2 REMARK 470 GLU A 13 OE1 OE2 REMARK 470 LYS A 19 CG CD CE NZ REMARK 470 ARG A 36 NE CZ NH1 NH2 REMARK 470 ARG A 46 CZ NH1 NH2 REMARK 470 GLU A 149 OE1 OE2 REMARK 470 ARG A 151 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 156 CG1 CG2 CD1 REMARK 470 GLU A 160 CG CD OE1 OE2 REMARK 470 LYS A 163 CG CD CE NZ REMARK 470 GLN A 164 CG CD OE1 NE2 REMARK 470 ARG A 171 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 178 CG CD CE NZ REMARK 470 GLU A 277 CG CD OE1 OE2 REMARK 470 LYS A 289 CE NZ REMARK 470 GLU A 291 CG CD OE1 OE2 REMARK 470 GLN A 295 CD OE1 NE2 REMARK 470 LYS A 298 CG CD CE NZ REMARK 470 LYS A 309 CG CD CE NZ REMARK 470 ARG A 319 NE CZ NH1 NH2 REMARK 470 GLU A 322 OE1 OE2 REMARK 470 ASP A 330 CG OD1 OD2 REMARK 470 ARG A 334 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 337 OE1 OE2 REMARK 470 GLN A 341 CG CD OE1 NE2 REMARK 470 GLN A 360 OE1 NE2 REMARK 470 LYS A 388 CE NZ REMARK 470 GLU A 396 OE1 OE2 REMARK 470 ARG B 36 NE CZ NH1 NH2 REMARK 470 GLU B 47 CD OE1 OE2 REMARK 470 ARG B 130 NE CZ NH1 NH2 REMARK 470 GLU B 146 CG CD OE1 OE2 REMARK 470 GLU B 149 CG CD OE1 OE2 REMARK 470 GLU B 154 CD OE1 OE2 REMARK 470 GLU B 160 CD OE1 OE2 REMARK 470 LYS B 163 CG CD CE NZ REMARK 470 GLN B 164 CG CD OE1 NE2 REMARK 470 GLU B 198 CD OE1 OE2 REMARK 470 ARG B 235 CD NE CZ NH1 NH2 REMARK 470 GLU B 277 CG CD OE1 OE2 REMARK 470 GLU B 291 CG CD OE1 OE2 REMARK 470 LYS B 298 CE NZ REMARK 470 GLU B 305 OE1 OE2 REMARK 470 LYS B 309 CE NZ REMARK 470 GLN B 321 OE1 NE2 REMARK 470 GLU B 331 CG CD OE1 OE2 REMARK 470 ARG B 334 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 341 CG CD OE1 NE2 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 NZ LYS B 38 O HOH B 483 1.47 REMARK 500 OG1 THR B 122 O HOH B 483 1.69 REMARK 500 OD2 ASP A 168 OD2 ASP A 170 2.05 REMARK 500 OE2 GLU B 318 O HOH B 489 2.12 REMARK 500 NE2 GLN B 9 O HOH B 431 2.15 REMARK 500 OE1 GLN B 9 O HOH B 485 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 NH1 ARG A 314 OE2 GLU B 322 1554 2.15 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 LEU A 350 CA - CB - CG ANGL. DEV. = 14.3 DEGREES REMARK 500 ARG B 6 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 LEU B 212 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 LEU B 350 CA - CB - CG ANGL. DEV. = 16.1 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 78 -136.41 -165.79 REMARK 500 ASP A 90 99.43 -63.82 REMARK 500 ASP A 123 70.22 49.77 REMARK 500 SER B 78 -149.17 176.62 REMARK 500 ASN B 85 75.43 -116.87 REMARK 500 ASP B 123 70.35 47.01 REMARK 500 ARG B 130 25.08 48.48 REMARK 500 GLU B 224 146.00 -172.30 REMARK 500 LEU B 265 114.19 -163.66 REMARK 500 ASP B 376 17.70 53.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 410 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 79 NE2 REMARK 620 2 ASP A 90 OD2 82.6 REMARK 620 3 HIS A 189 NE2 117.0 71.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 411 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 90 OD2 REMARK 620 2 HIS B 189 NE2 77.5 REMARK 620 3 HIS B 79 NE2 76.5 122.0 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA B 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAC B 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 411 DBREF 3N5F A 1 408 UNP Q53389 AMAB2_BACST 1 408 DBREF 3N5F B 1 408 UNP Q53389 AMAB2_BACST 1 408 SEQRES 1 A 408 MET ILE GLN GLY GLU ARG LEU TRP GLN ARG LEU MET GLU SEQRES 2 A 408 LEU GLY GLU VAL GLY LYS GLN PRO SER GLY GLY VAL THR SEQRES 3 A 408 ARG LEU SER PHE THR ALA GLU GLU ARG ARG ALA LYS ASP SEQRES 4 A 408 LEU VAL ALA SER TYR MET ARG GLU ALA GLY LEU PHE VAL SEQRES 5 A 408 TYR GLU ASP ALA ALA GLY ASN LEU ILE GLY ARG LYS GLU SEQRES 6 A 408 GLY THR ASN PRO ASP ALA THR VAL VAL LEU VAL GLY SER SEQRES 7 A 408 HIS LEU ASP SER VAL TYR ASN GLY GLY CYS PHE ASP GLY SEQRES 8 A 408 PRO LEU GLY VAL LEU ALA GLY VAL GLU VAL VAL GLN THR SEQRES 9 A 408 MET ASN GLU HIS GLY VAL VAL THR HIS HIS PRO ILE GLU SEQRES 10 A 408 VAL VAL ALA PHE THR ASP GLU GLU GLY ALA ARG PHE ARG SEQRES 11 A 408 PHE GLY MET ILE GLY SER ARG ALA MET ALA GLY THR LEU SEQRES 12 A 408 PRO PRO GLU ALA LEU GLU CYS ARG ASP ALA GLU GLY ILE SEQRES 13 A 408 SER LEU ALA GLU ALA MET LYS GLN ALA GLY LEU ASP PRO SEQRES 14 A 408 ASP ARG LEU PRO GLN ALA ALA ARG LYS PRO GLY THR VAL SEQRES 15 A 408 LYS ALA TYR VAL GLU LEU HIS ILE GLU GLN GLY ARG VAL SEQRES 16 A 408 LEU GLU GLU THR GLY LEU PRO VAL GLY ILE VAL THR GLY SEQRES 17 A 408 ILE ALA GLY LEU ILE TRP VAL LYS PHE THR ILE GLU GLY SEQRES 18 A 408 LYS ALA GLU HIS ALA GLY ALA THR PRO MET SER LEU ARG SEQRES 19 A 408 ARG ASP PRO MET ALA ALA ALA ALA GLN ILE ILE ILE VAL SEQRES 20 A 408 ILE GLU GLU GLU ALA ARG ARG THR GLY THR THR VAL GLY SEQRES 21 A 408 THR VAL GLY GLN LEU HIS VAL TYR PRO GLY GLY ILE ASN SEQRES 22 A 408 VAL ILE PRO GLU ARG VAL GLU PHE VAL LEU ASP LEU ARG SEQRES 23 A 408 ASP LEU LYS ALA GLU VAL ARG ASP GLN VAL TRP LYS ALA SEQRES 24 A 408 ILE ALA VAL ARG ALA GLU THR ILE ALA LYS GLU ARG ASN SEQRES 25 A 408 VAL ARG VAL THR THR GLU ARG LEU GLN GLU MET PRO PRO SEQRES 26 A 408 VAL LEU CYS SER ASP GLU VAL LYS ARG ALA ALA GLU ALA SEQRES 27 A 408 ALA CYS GLN LYS LEU GLY TYR PRO SER PHE TRP LEU PRO SEQRES 28 A 408 SER GLY ALA ALA HIS ASP SER VAL GLN LEU ALA PRO ILE SEQRES 29 A 408 CYS PRO ILE GLY MET ILE PHE VAL ARG SER GLN ASP GLY SEQRES 30 A 408 VAL SER HIS SER PRO ALA GLU TRP SER THR LYS GLU ASP SEQRES 31 A 408 CYS ALA ALA GLY ALA GLU VAL LEU TYR HIS THR VAL TRP SEQRES 32 A 408 GLN LEU ALA GLN GLY SEQRES 1 B 408 MET ILE GLN GLY GLU ARG LEU TRP GLN ARG LEU MET GLU SEQRES 2 B 408 LEU GLY GLU VAL GLY LYS GLN PRO SER GLY GLY VAL THR SEQRES 3 B 408 ARG LEU SER PHE THR ALA GLU GLU ARG ARG ALA LYS ASP SEQRES 4 B 408 LEU VAL ALA SER TYR MET ARG GLU ALA GLY LEU PHE VAL SEQRES 5 B 408 TYR GLU ASP ALA ALA GLY ASN LEU ILE GLY ARG LYS GLU SEQRES 6 B 408 GLY THR ASN PRO ASP ALA THR VAL VAL LEU VAL GLY SER SEQRES 7 B 408 HIS LEU ASP SER VAL TYR ASN GLY GLY CYS PHE ASP GLY SEQRES 8 B 408 PRO LEU GLY VAL LEU ALA GLY VAL GLU VAL VAL GLN THR SEQRES 9 B 408 MET ASN GLU HIS GLY VAL VAL THR HIS HIS PRO ILE GLU SEQRES 10 B 408 VAL VAL ALA PHE THR ASP GLU GLU GLY ALA ARG PHE ARG SEQRES 11 B 408 PHE GLY MET ILE GLY SER ARG ALA MET ALA GLY THR LEU SEQRES 12 B 408 PRO PRO GLU ALA LEU GLU CYS ARG ASP ALA GLU GLY ILE SEQRES 13 B 408 SER LEU ALA GLU ALA MET LYS GLN ALA GLY LEU ASP PRO SEQRES 14 B 408 ASP ARG LEU PRO GLN ALA ALA ARG LYS PRO GLY THR VAL SEQRES 15 B 408 LYS ALA TYR VAL GLU LEU HIS ILE GLU GLN GLY ARG VAL SEQRES 16 B 408 LEU GLU GLU THR GLY LEU PRO VAL GLY ILE VAL THR GLY SEQRES 17 B 408 ILE ALA GLY LEU ILE TRP VAL LYS PHE THR ILE GLU GLY SEQRES 18 B 408 LYS ALA GLU HIS ALA GLY ALA THR PRO MET SER LEU ARG SEQRES 19 B 408 ARG ASP PRO MET ALA ALA ALA ALA GLN ILE ILE ILE VAL SEQRES 20 B 408 ILE GLU GLU GLU ALA ARG ARG THR GLY THR THR VAL GLY SEQRES 21 B 408 THR VAL GLY GLN LEU HIS VAL TYR PRO GLY GLY ILE ASN SEQRES 22 B 408 VAL ILE PRO GLU ARG VAL GLU PHE VAL LEU ASP LEU ARG SEQRES 23 B 408 ASP LEU LYS ALA GLU VAL ARG ASP GLN VAL TRP LYS ALA SEQRES 24 B 408 ILE ALA VAL ARG ALA GLU THR ILE ALA LYS GLU ARG ASN SEQRES 25 B 408 VAL ARG VAL THR THR GLU ARG LEU GLN GLU MET PRO PRO SEQRES 26 B 408 VAL LEU CYS SER ASP GLU VAL LYS ARG ALA ALA GLU ALA SEQRES 27 B 408 ALA CYS GLN LYS LEU GLY TYR PRO SER PHE TRP LEU PRO SEQRES 28 B 408 SER GLY ALA ALA HIS ASP SER VAL GLN LEU ALA PRO ILE SEQRES 29 B 408 CYS PRO ILE GLY MET ILE PHE VAL ARG SER GLN ASP GLY SEQRES 30 B 408 VAL SER HIS SER PRO ALA GLU TRP SER THR LYS GLU ASP SEQRES 31 B 408 CYS ALA ALA GLY ALA GLU VAL LEU TYR HIS THR VAL TRP SEQRES 32 B 408 GLN LEU ALA GLN GLY HET IPA A 409 4 HET CO A 410 1 HET IPA B 409 4 HET CAC B 410 5 HET CO B 411 1 HETNAM IPA ISOPROPYL ALCOHOL HETNAM CO COBALT (II) ION HETNAM CAC CACODYLATE ION HETSYN IPA 2-PROPANOL HETSYN CAC DIMETHYLARSINATE FORMUL 3 IPA 2(C3 H8 O) FORMUL 4 CO 2(CO 2+) FORMUL 6 CAC C2 H6 AS O2 1- FORMUL 8 HOH *128(H2 O) HELIX 1 1 GLN A 3 GLU A 16 1 14 HELIX 2 2 THR A 31 GLY A 49 1 19 HELIX 3 3 GLY A 91 HIS A 108 1 18 HELIX 4 4 MET A 133 GLY A 141 1 9 HELIX 5 5 PRO A 144 GLU A 149 5 6 HELIX 6 6 SER A 157 ALA A 165 1 9 HELIX 7 7 ASP A 168 ALA A 176 5 9 HELIX 8 8 ARG A 194 GLY A 200 1 7 HELIX 9 9 ASP A 236 GLY A 256 1 21 HELIX 10 10 LYS A 289 ASN A 312 1 24 HELIX 11 11 SER A 329 GLY A 344 1 16 HELIX 12 12 SER A 374 VAL A 378 5 5 HELIX 13 13 THR A 387 ALA A 406 1 20 HELIX 14 14 GLY B 4 GLY B 15 1 12 HELIX 15 15 THR B 31 ALA B 48 1 18 HELIX 16 16 GLY B 91 HIS B 108 1 18 HELIX 17 17 MET B 133 GLY B 141 1 9 HELIX 18 18 PRO B 144 CYS B 150 5 7 HELIX 19 19 SER B 157 ALA B 165 1 9 HELIX 20 20 ASP B 168 ALA B 176 5 9 HELIX 21 21 ARG B 194 GLY B 200 1 7 HELIX 22 22 PRO B 230 ARG B 234 5 5 HELIX 23 23 ASP B 236 THR B 255 1 20 HELIX 24 24 LYS B 289 ASN B 312 1 24 HELIX 25 25 SER B 329 GLY B 344 1 16 HELIX 26 26 ASP B 357 ALA B 362 1 6 HELIX 27 27 SER B 374 VAL B 378 5 5 HELIX 28 28 THR B 387 ALA B 406 1 20 SHEET 1 A 8 PHE A 51 GLU A 54 0 SHEET 2 A 8 LEU A 60 LYS A 64 -1 O ILE A 61 N TYR A 53 SHEET 3 A 8 ILE A 116 PHE A 121 -1 O ILE A 116 N LYS A 64 SHEET 4 A 8 VAL A 73 HIS A 79 1 N VAL A 76 O VAL A 119 SHEET 5 A 8 VAL A 182 ILE A 190 1 O ALA A 184 N LEU A 75 SHEET 6 A 8 ILE A 367 VAL A 372 1 O ILE A 370 N HIS A 189 SHEET 7 A 8 VAL A 203 ILE A 209 -1 N GLY A 204 O PHE A 371 SHEET 8 A 8 VAL A 326 LEU A 327 -1 O VAL A 326 N ILE A 209 SHEET 1 B 8 PHE A 51 GLU A 54 0 SHEET 2 B 8 LEU A 60 LYS A 64 -1 O ILE A 61 N TYR A 53 SHEET 3 B 8 ILE A 116 PHE A 121 -1 O ILE A 116 N LYS A 64 SHEET 4 B 8 VAL A 73 HIS A 79 1 N VAL A 76 O VAL A 119 SHEET 5 B 8 VAL A 182 ILE A 190 1 O ALA A 184 N LEU A 75 SHEET 6 B 8 ILE A 367 VAL A 372 1 O ILE A 370 N HIS A 189 SHEET 7 B 8 VAL A 203 ILE A 209 -1 N GLY A 204 O PHE A 371 SHEET 8 B 8 TRP A 349 SER A 352 1 O SER A 352 N GLY A 208 SHEET 1 C 4 VAL A 259 TYR A 268 0 SHEET 2 C 4 ARG A 278 ASP A 287 -1 O ASP A 284 N THR A 261 SHEET 3 C 4 GLY A 211 GLU A 220 -1 N GLY A 211 O ASP A 287 SHEET 4 C 4 ARG A 314 MET A 323 -1 O LEU A 320 N TRP A 214 SHEET 1 D 2 GLU A 224 HIS A 225 0 SHEET 2 D 2 VAL A 274 ILE A 275 -1 O ILE A 275 N GLU A 224 SHEET 1 E 8 PHE B 51 GLU B 54 0 SHEET 2 E 8 LEU B 60 LYS B 64 -1 O ILE B 61 N TYR B 53 SHEET 3 E 8 ILE B 116 PHE B 121 -1 O VAL B 118 N GLY B 62 SHEET 4 E 8 VAL B 73 HIS B 79 1 N VAL B 76 O GLU B 117 SHEET 5 E 8 VAL B 182 ILE B 190 1 O ALA B 184 N LEU B 75 SHEET 6 E 8 ILE B 367 VAL B 372 1 O ILE B 370 N HIS B 189 SHEET 7 E 8 VAL B 203 ILE B 209 -1 N GLY B 204 O PHE B 371 SHEET 8 E 8 VAL B 326 LEU B 327 -1 O VAL B 326 N ILE B 209 SHEET 1 F 8 PHE B 51 GLU B 54 0 SHEET 2 F 8 LEU B 60 LYS B 64 -1 O ILE B 61 N TYR B 53 SHEET 3 F 8 ILE B 116 PHE B 121 -1 O VAL B 118 N GLY B 62 SHEET 4 F 8 VAL B 73 HIS B 79 1 N VAL B 76 O GLU B 117 SHEET 5 F 8 VAL B 182 ILE B 190 1 O ALA B 184 N LEU B 75 SHEET 6 F 8 ILE B 367 VAL B 372 1 O ILE B 370 N HIS B 189 SHEET 7 F 8 VAL B 203 ILE B 209 -1 N GLY B 204 O PHE B 371 SHEET 8 F 8 TRP B 349 SER B 352 1 O SER B 352 N GLY B 208 SHEET 1 G 4 VAL B 259 TYR B 268 0 SHEET 2 G 4 ARG B 278 ASP B 287 -1 O ASP B 284 N THR B 261 SHEET 3 G 4 GLY B 211 GLU B 220 -1 N PHE B 217 O PHE B 281 SHEET 4 G 4 ARG B 314 MET B 323 -1 O LEU B 320 N TRP B 214 SHEET 1 H 2 GLU B 224 HIS B 225 0 SHEET 2 H 2 VAL B 274 ILE B 275 -1 O ILE B 275 N GLU B 224 LINK NE2 HIS A 79 CO CO A 410 1555 1555 2.09 LINK OD2 ASP B 90 CO CO B 411 1555 1555 2.11 LINK OD2 ASP A 90 CO CO A 410 1555 1555 2.18 LINK NE2 HIS B 189 CO CO B 411 1555 1555 2.23 LINK NE2 HIS A 189 CO CO A 410 1555 1555 2.31 LINK NE2 HIS B 79 CO CO B 411 1555 1555 2.35 CISPEP 1 TYR A 268 PRO A 269 0 7.04 CISPEP 2 TYR B 268 PRO B 269 0 5.61 SITE 1 AC1 3 GLY A 227 THR B 257 PRO B 351 SITE 1 AC2 4 HIS A 79 ASP A 90 GLU A 124 HIS A 189 SITE 1 AC3 3 LEU B 50 ARG B 303 THR B 306 SITE 1 AC4 5 HIS A 225 ASN A 273 ALA B 354 ALA B 355 SITE 2 AC4 5 HIS B 380 SITE 1 AC5 4 HIS B 79 ASP B 90 GLU B 124 HIS B 189 CRYST1 103.208 211.683 43.091 90.00 90.00 90.00 P 21 21 2 8 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 0.009689 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004724 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023207 0.00000 MASTER 434 0 5 28 44 0 6 6 0 0 0 64 END