HEADER HYDROLASE 31-JUL-09 3IIB TITLE CRYSTAL STRUCTURE OF PEPTIDASE M28 PRECURSOR (YP_926796.1) FROM TITLE 2 SHEWANELLA AMAZONENSIS SB2B AT 1.70 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDASE M28; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA AMAZONENSIS SB2B; SOURCE 3 ORGANISM_TAXID: 326297; SOURCE 4 GENE: SAMA_0919, YP_926796.1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS YP_926796.1, PEPTIDASE M28 PRECURSOR, STRUCTURAL GENOMICS, JOINT KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 PSI-2, PEPTIDASE FAMILY M28, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3IIB 1 REMARK SEQADV LINK REVDAT 4 24-JUL-19 3IIB 1 REMARK LINK REVDAT 3 01-NOV-17 3IIB 1 REMARK REVDAT 2 13-JUL-11 3IIB 1 VERSN REVDAT 1 25-AUG-09 3IIB 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PEPTIDASE M28 PRECURSOR (YP_926796.1) JRNL TITL 2 FROM SHEWANELLA AMAZONENSIS SB2B AT 1.70 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0053 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 58229 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) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2960 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4019 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 207 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3283 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 631 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 10.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : -0.17000 REMARK 3 B33 (A**2) : -0.19000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.34000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.084 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.086 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.559 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3459 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2302 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4721 ; 1.471 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5676 ; 0.909 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 474 ; 6.448 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;36.001 ;24.965 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 567 ;11.636 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;19.140 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 543 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3938 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 640 ; 0.001 ; 0.020 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): 2244 ; 1.640 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 916 ; 0.530 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3611 ; 2.466 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1215 ; 4.048 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1093 ; 6.271 ;11.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 25 A 466 REMARK 3 ORIGIN FOR THE GROUP (A): 1.1964 12.5565 20.4912 REMARK 3 T TENSOR REMARK 3 T11: 0.0087 T22: 0.0022 REMARK 3 T33: 0.0156 T12: -0.0009 REMARK 3 T13: 0.0051 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.1584 L22: 0.1537 REMARK 3 L33: 0.4015 L12: 0.0770 REMARK 3 L13: 0.1582 L23: 0.0697 REMARK 3 S TENSOR REMARK 3 S11: 0.0067 S12: -0.0107 S13: 0.0111 REMARK 3 S21: 0.0196 S22: -0.0026 S23: 0.0042 REMARK 3 S31: 0.0133 S32: -0.0245 S33: -0.0040 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: 1.HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS REMARK 3 ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE REMARK 3 ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED REMARK 3 SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.ZINC (ZN) REMARK 3 HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON A REMARK 3 FLUORESCENCE EXCITATION SCAN AND THE ANOMALOUS DIFFERENCE REMARK 3 FOURIER MAP. 5.THERE IS A CIS-PEPTIDE BOND BETWEEN RESIDUES REMARK 3 ASP292 AND ASP293 AT THE PUTATIVE ACTIVE SITE. 6.PEG FRAGMENTS REMARK 3 (PEG AND PGE) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN REMARK 3 MODELED IN THE SOLVENT STRUCTURE. REMARK 4 REMARK 4 3IIB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054446. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91837,0.97791 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(111) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.5 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58230 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 29.374 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : 0.12000 REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.46200 REMARK 200 R SYM FOR SHELL (I) : 0.46200 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2000M MGCL2, 30.0000% PEG-400, 0.1M REMARK 280 TRIS PH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 45.22100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.43350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.22100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 42.43350 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: CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER REMARK 300 AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -145.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 480 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 621 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 629 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 GLY A 0 REMARK 465 GLU A 467 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 GLU A 65 CD OE1 OE2 REMARK 470 ARG A 97 CD NE CZ NH1 NH2 REMARK 470 GLN A 127 CG CD OE1 NE2 REMARK 470 LYS A 237 CE NZ REMARK 470 LYS A 338 CD CE NZ REMARK 470 LYS A 393 CG CD CE NZ REMARK 470 GLU A 437 CD OE1 OE2 REMARK 470 LYS A 457 CE NZ REMARK 470 LYS A 466 CG CD CE NZ 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 OD1 ASN A 377 O HOH A 843 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 889 O HOH A 891 2656 2.17 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 VAL A 57 -57.32 -124.30 REMARK 500 SER A 268 -93.47 -134.41 REMARK 500 ASP A 354 54.28 -156.11 REMARK 500 PHE A 355 45.33 -143.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PEG A 5 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 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 292 OD2 REMARK 620 2 GLU A 327 OE1 140.1 REMARK 620 3 GLU A 327 OE2 84.2 57.7 REMARK 620 4 HIS A 425 NE2 87.6 88.1 100.2 REMARK 620 5 HOH A 589 O 101.2 93.3 93.7 164.3 REMARK 620 6 HOH A 648 O 109.7 110.0 163.3 89.9 74.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 280 NE2 REMARK 620 2 ASP A 292 OD1 87.2 REMARK 620 3 ASP A 354 OD1 85.1 97.0 REMARK 620 4 ASP A 354 OD2 92.0 154.7 57.8 REMARK 620 5 HOH A 587 O 171.7 98.7 88.4 80.2 REMARK 620 6 HOH A 589 O 98.4 97.6 165.1 107.5 86.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 396409 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT INCLUDING RESIDUES 25-467 WAS EXPRESSED WITH A REMARK 999 PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV REMARK 999 PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3IIB A 25 467 UNP A1S420 A1S420_SHEAM 25 467 SEQADV 3IIB GLY A 0 UNP A1S420 EXPRESSION TAG SEQRES 1 A 444 GLY SER ASP ASP ILE ASN GLN LYS VAL ALA GLU GLN LEU SEQRES 2 A 444 ALA GLN LYS ALA GLN SER SER SER LEU GLY TYR ASP ILE SEQRES 3 A 444 VAL GLU SER LEU THR VAL GLU VAL GLY PRO ARG LEU ALA SEQRES 4 A 444 GLY SER GLU GLN ASP LYS VAL ALA VAL ASP TRP ALA ILE SEQRES 5 A 444 ALA LYS LEU GLN SER LEU GLY PHE ASP ARG VAL TYR LYS SEQRES 6 A 444 GLU PRO VAL THR VAL PRO VAL TRP ARG ARG GLY ILE ALA SEQRES 7 A 444 LYS ALA SER ILE LEU SER PRO PHE PRO GLN PRO LEU VAL SEQRES 8 A 444 VAL THR ALA LEU GLY GLY SER ILE ALA THR PRO ALA GLN SEQRES 9 A 444 GLY LEU SER ALA THR ILE VAL ARG PHE ASP THR LEU GLN SEQRES 10 A 444 ASP LEU GLN ASN ALA GLU ALA GLY SER LEU ASN ASP LYS SEQRES 11 A 444 ILE ALA PHE ILE ASP ALA LYS THR GLU ARG HIS ARG ASP SEQRES 12 A 444 GLY LYS GLY TYR GLY GLN THR ALA SER GLY ARG SER ARG SEQRES 13 A 444 GLY ALA VAL ALA ALA ALA GLU LYS GLY ALA VAL GLY ILE SEQRES 14 A 444 ILE ILE ARG SER ILE GLY THR ASP HIS ASP ARG MSE ALA SEQRES 15 A 444 HIS THR GLY MSE MSE ARG TYR GLU GLU GLY VAL THR ALA SEQRES 16 A 444 ILE PRO ALA ALA ALA ILE SER ASN PRO ASP ALA ASP LEU SEQRES 17 A 444 ILE ASN ALA MSE LEU LYS ARG ASP LYS GLU VAL VAL ILE SEQRES 18 A 444 SER LEU GLU LEU GLY SER GLU ARG ARG GLY GLU THR THR SEQRES 19 A 444 SER TYR ASN VAL ILE ALA GLU VAL LYS GLY SER THR LYS SEQRES 20 A 444 ALA ASP GLU ILE VAL LEU ILE GLY ALA HIS LEU ASP SER SEQRES 21 A 444 TRP ASP GLU GLY THR GLY ALA ILE ASP ASP GLY ALA GLY SEQRES 22 A 444 VAL ALA ILE VAL THR ALA ALA ALA LYS HIS ILE LEU ASP SEQRES 23 A 444 LEU PRO GLN LYS PRO GLU ARG THR ILE ARG VAL VAL LEU SEQRES 24 A 444 TYR ALA ALA GLU GLU LEU GLY LEU LEU GLY GLY LYS THR SEQRES 25 A 444 TYR ALA LYS GLU HIS GLU ALA GLU LEU GLU LYS HIS TYR SEQRES 26 A 444 ILE ALA ALA GLU SER ASP PHE GLY ALA GLY PRO ILE TYR SEQRES 27 A 444 GLN ILE ASP TRP ARG VAL ALA ASP THR ALA HIS SER PRO SEQRES 28 A 444 VAL ILE ASN ALA MSE LYS VAL ALA GLU PRO LEU GLY VAL SEQRES 29 A 444 ALA ALA GLY ASN ASN LYS ALA SER GLY GLY PRO ASP VAL SEQRES 30 A 444 SER MSE LEU PRO ALA LEU GLY VAL PRO VAL ALA SER LEU SEQRES 31 A 444 ARG GLN ASP GLY SER ASP TYR PHE ASP TYR HIS HIS THR SEQRES 32 A 444 PRO ASN ASP THR LEU ASP LYS ILE ASN PRO GLU ALA LEU SEQRES 33 A 444 ALA GLN ASN VAL ALA VAL TYR ALA GLN PHE ALA TRP VAL SEQRES 34 A 444 MSE ALA ASN SER LYS VAL GLU LEU ARG PRO LEU PRO PRO SEQRES 35 A 444 LYS GLU MODRES 3IIB MSE A 204 MET SELENOMETHIONINE MODRES 3IIB MSE A 209 MET SELENOMETHIONINE MODRES 3IIB MSE A 210 MET SELENOMETHIONINE MODRES 3IIB MSE A 235 MET SELENOMETHIONINE MODRES 3IIB MSE A 379 MET SELENOMETHIONINE MODRES 3IIB MSE A 402 MET SELENOMETHIONINE MODRES 3IIB MSE A 453 MET SELENOMETHIONINE HET MSE A 204 8 HET MSE A 209 8 HET MSE A 210 8 HET MSE A 235 8 HET MSE A 379 8 HET MSE A 402 8 HET MSE A 453 8 HET ZN A 1 1 HET ZN A 2 1 HET PGE A 3 10 HET PEG A 4 7 HET PEG A 5 5 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM PGE TRIETHYLENE GLYCOL HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 1 MSE 7(C5 H11 N O2 SE) FORMUL 2 ZN 2(ZN 2+) FORMUL 4 PGE C6 H14 O4 FORMUL 5 PEG 2(C4 H10 O3) FORMUL 7 HOH *631(H2 O) HELIX 1 1 SER A 25 SER A 43 1 19 HELIX 2 2 SER A 44 VAL A 57 1 14 HELIX 3 3 SER A 64 LEU A 81 1 18 HELIX 4 4 THR A 138 ASN A 144 1 7 HELIX 5 5 GLY A 167 LYS A 187 1 21 HELIX 6 6 SER A 225 LYS A 237 1 13 HELIX 7 7 ASP A 293 ASP A 309 1 17 HELIX 8 8 ALA A 325 GLY A 329 5 5 HELIX 9 9 LEU A 330 HIS A 340 1 11 HELIX 10 10 GLU A 341 GLU A 345 5 5 HELIX 11 11 ALA A 368 THR A 370 5 3 HELIX 12 12 ALA A 371 MSE A 379 1 9 HELIX 13 13 LYS A 380 GLY A 386 5 7 HELIX 14 14 GLY A 397 SER A 401 5 5 HELIX 15 15 LEU A 403 GLY A 407 5 5 HELIX 16 16 ASP A 419 TYR A 423 5 5 HELIX 17 17 THR A 430 ILE A 434 5 5 HELIX 18 18 ASN A 435 SER A 456 1 22 SHEET 1 A 8 GLN A 111 LEU A 113 0 SHEET 2 A 8 ARG A 85 SER A 107 -1 N ILE A 105 O GLN A 111 SHEET 3 A 8 VAL A 243 VAL A 265 -1 O ILE A 262 N TYR A 87 SHEET 4 A 8 LEU A 129 PHE A 136 -1 N LEU A 129 O LEU A 246 SHEET 5 A 8 ILE A 154 ILE A 157 1 O PHE A 156 N PHE A 136 SHEET 6 A 8 GLY A 191 ARG A 195 1 O ARG A 195 N ILE A 157 SHEET 7 A 8 ALA A 221 ILE A 224 1 O ILE A 224 N ILE A 194 SHEET 8 A 8 VAL A 115 ALA A 117 -1 N THR A 116 O ALA A 223 SHEET 1 B 6 GLN A 111 LEU A 113 0 SHEET 2 B 6 ARG A 85 SER A 107 -1 N ILE A 105 O GLN A 111 SHEET 3 B 6 VAL A 243 VAL A 265 -1 O ILE A 262 N TYR A 87 SHEET 4 B 6 ARG A 316 TYR A 323 -1 O VAL A 320 N ALA A 263 SHEET 5 B 6 LYS A 270 HIS A 280 1 N VAL A 275 O ARG A 319 SHEET 6 B 6 HIS A 347 GLU A 352 1 O TYR A 348 N ILE A 274 SHEET 1 C 3 ALA A 388 ALA A 389 0 SHEET 2 C 3 ILE A 360 ARG A 366 1 N TYR A 361 O ALA A 388 SHEET 3 C 3 VAL A 410 GLN A 415 -1 O SER A 412 N ASP A 364 LINK C ARG A 203 N MSE A 204 1555 1555 1.34 LINK C MSE A 204 N ALA A 205 1555 1555 1.34 LINK C GLY A 208 N MSE A 209 1555 1555 1.32 LINK C MSE A 209 N MSE A 210 1555 1555 1.32 LINK C MSE A 210 N ARG A 211 1555 1555 1.33 LINK C ALA A 234 N MSE A 235 1555 1555 1.33 LINK C MSE A 235 N LEU A 236 1555 1555 1.35 LINK C ALA A 378 N MSE A 379 1555 1555 1.34 LINK C MSE A 379 N LYS A 380 1555 1555 1.33 LINK C SER A 401 N MSE A 402 1555 1555 1.35 LINK C MSE A 402 N LEU A 403 1555 1555 1.32 LINK C VAL A 452 N MSE A 453 1555 1555 1.33 LINK C MSE A 453 N ALA A 454 1555 1555 1.34 LINK ZN ZN A 1 OD2 ASP A 292 1555 1555 2.03 LINK ZN ZN A 1 OE1 GLU A 327 1555 1555 2.22 LINK ZN ZN A 1 OE2 GLU A 327 1555 1555 2.35 LINK ZN ZN A 1 NE2 HIS A 425 1555 1555 2.28 LINK ZN ZN A 1 O HOH A 589 1555 1555 2.13 LINK ZN ZN A 1 O HOH A 648 1555 1555 2.13 LINK ZN ZN A 2 NE2 HIS A 280 1555 1555 2.17 LINK ZN ZN A 2 OD1 ASP A 292 1555 1555 2.08 LINK ZN ZN A 2 OD1 ASP A 354 1555 1555 2.15 LINK ZN ZN A 2 OD2 ASP A 354 1555 1555 2.33 LINK ZN ZN A 2 O HOH A 587 1555 1555 2.38 LINK ZN ZN A 2 O HOH A 589 1555 1555 1.95 CISPEP 1 SER A 107 PRO A 108 0 6.86 CISPEP 2 SER A 107 PRO A 108 0 4.25 CISPEP 3 ASP A 292 ASP A 293 0 1.96 CISPEP 4 ARG A 461 PRO A 462 0 -4.28 SITE 1 AC1 7 ZN A 2 ASP A 292 GLU A 327 HIS A 424 SITE 2 AC1 7 HIS A 425 HOH A 589 HOH A 648 SITE 1 AC2 6 ZN A 1 HIS A 280 ASP A 292 ASP A 354 SITE 2 AC2 6 HOH A 587 HOH A 589 SITE 1 AC3 5 LEU A 45 SER A 80 LEU A 81 LYS A 305 SITE 2 AC3 5 ASP A 309 SITE 1 AC4 3 ARG A 135 ASN A 233 LYS A 237 CRYST1 90.442 84.867 80.114 90.00 115.85 90.00 C 1 2 1 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 0.011057 0.000000 0.005358 0.00000 SCALE2 0.000000 0.011783 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013870 0.00000