10 20 30 40 50 60 70 80 2HIP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSFER (IRON-SULFUR PROTEIN) 24-JUN-91 2HIP
TITLE THE MOLECULAR STRUCTURE OF THE HIGH POTENTIAL IRON-SULFUR TITLE 2 PROTEIN ISOLATED FROM ECTOTHIORHODOSPIRA HALOPHILA TITLE 3 DETERMINED AT 2.5-ANGSTROMS RESOLUTION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH POTENTIAL IRON SULFUR PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALORHODOSPIRA HALOPHILA; SOURCE 3 ORGANISM_TAXID: 1053
KEYWDS ELECTRON TRANSFER (IRON-SULFUR PROTEIN)
EXPDTA X-RAY DIFFRACTION
AUTHOR D.R.BREITER,T.E.MEYER,I.RAYMENT,H.M.HOLDEN
REVDAT 4 24-MAR-09 2HIP 1 ATOM CONECT REVDAT 3 24-FEB-09 2HIP 1 VERSN REVDAT 2 01-APR-03 2HIP 1 JRNL REVDAT 1 15-JUL-92 2HIP 0
JRNL AUTH D.R.BREITER,T.E.MEYER,I.RAYMENT,H.M.HOLDEN JRNL TITL THE MOLECULAR STRUCTURE OF THE HIGH POTENTIAL JRNL TITL 2 IRON-SULFUR PROTEIN ISOLATED FROM JRNL TITL 3 ECTOTHIORHODOSPIRA HALOPHILA DETERMINED AT 2.5-A JRNL TITL 4 RESOLUTION. JRNL REF J.BIOL.CHEM. V. 266 18660 1991 JRNL REFN ISSN 0021-9258 JRNL PMID 1917989
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1104 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.014 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.221 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2HIP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 15.97000 REMARK 290 SMTRY3 2 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: DIMERIC 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 SER A 72 REMARK 465 SER B 72
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 SG CYS B 64 FE4 SF4 B 73 1.66 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 ASP A 6 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 6 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 11 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 24 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 52 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 PHE A 53 CB - CG - CD2 ANGL. DEV. = 4.8 DEGREES REMARK 500 PHE A 53 CB - CG - CD1 ANGL. DEV. = -5.1 DEGREES REMARK 500 ASP A 54 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP B 6 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 43 CB - CG - OD2 ANGL. DEV. = -5.6 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 20 -17.29 -45.40 REMARK 500 GLU A 39 163.53 70.96 REMARK 500 ASP A 43 91.35 -59.31 REMARK 500 ALA A 60 -39.51 -38.52 REMARK 500 SER B 20 -60.79 -28.76 REMARK 500 VAL B 41 -90.59 -122.47 REMARK 500 SER B 65 -3.90 -56.44 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 ASP A 54 23.4 L L OUTSIDE RANGE REMARK 500 ASP B 54 16.8 L L OUTSIDE RANGE REMARK 500 VAL B 66 16.6 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 A 104 DISTANCE = 5.73 ANGSTROMS REMARK 525 HOH A 106 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH B 116 DISTANCE = 5.76 ANGSTROMS REMARK 525 HOH A 117 DISTANCE = 7.01 ANGSTROMS REMARK 525 HOH A 118 DISTANCE = 5.64 ANGSTROMS REMARK 525 HOH B 123 DISTANCE = 5.24 ANGSTROMS REMARK 525 HOH A 126 DISTANCE = 9.37 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 73 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 B 73
DBREF 2HIP A 1 71 UNP P04168 HIP1_ECTHA 1 71 DBREF 2HIP B 1 71 UNP P04168 HIP1_ECTHA 1 71
SEQRES 1 A 72 GLU PRO ARG ALA GLU ASP GLY HIS ALA HIS ASP TYR VAL SEQRES 2 A 72 ASN GLU ALA ALA ASP ALA SER GLY HIS PRO ARG TYR GLN SEQRES 3 A 72 GLU GLY GLN LEU CYS GLU ASN CYS ALA PHE TRP GLY GLU SEQRES 4 A 72 ALA VAL GLN ASP GLY TRP GLY ARG CYS THR HIS PRO ASP SEQRES 5 A 72 PHE ASP GLU VAL LEU VAL LYS ALA GLU GLY TRP CYS SER SEQRES 6 A 72 VAL TYR ALA PRO ALA SER SER SEQRES 1 B 72 GLU PRO ARG ALA GLU ASP GLY HIS ALA HIS ASP TYR VAL SEQRES 2 B 72 ASN GLU ALA ALA ASP ALA SER GLY HIS PRO ARG TYR GLN SEQRES 3 B 72 GLU GLY GLN LEU CYS GLU ASN CYS ALA PHE TRP GLY GLU SEQRES 4 B 72 ALA VAL GLN ASP GLY TRP GLY ARG CYS THR HIS PRO ASP SEQRES 5 B 72 PHE ASP GLU VAL LEU VAL LYS ALA GLU GLY TRP CYS SER SEQRES 6 B 72 VAL TYR ALA PRO ALA SER SER
HET SF4 A 73 8 HET SF4 B 73 8
HETNAM SF4 IRON/SULFUR CLUSTER
FORMUL 3 SF4 2(FE4 S4) FORMUL 5 HOH *104(H2 O)
HELIX 1 1 GLU A 15 SER A 20 5 6 HELIX 2 2 LEU A 30 ASN A 33 5 4 HELIX 3 3 HIS A 50 ASP A 54 5 5 HELIX 4 4 GLU B 15 SER B 20 5 6 HELIX 5 5 LEU B 30 ASN B 33 5 4 HELIX 6 6 HIS B 50 ASP B 54 5 5
SHEET 1 A 3 TRP A 37 GLN A 42 0 SHEET 2 A 3 TRP A 45 CYS A 48 -1 O TRP A 45 N VAL A 41 SHEET 3 A 3 VAL A 58 LYS A 59 -1 N VAL A 58 O GLY A 46 SHEET 1 B 3 TRP B 37 ALA B 40 0 SHEET 2 B 3 TRP B 45 CYS B 48 -1 O ARG B 47 N GLY B 38 SHEET 3 B 3 VAL B 58 LYS B 59 -1 O VAL B 58 N GLY B 46
LINK SG CYS A 31 FE1 SF4 A 73 1555 1555 2.18 LINK SG CYS A 34 FE2 SF4 A 73 1555 1555 2.41 LINK SG CYS A 48 FE3 SF4 A 73 1555 1555 2.09 LINK SG CYS A 64 FE4 SF4 A 73 1555 1555 2.02 LINK SG CYS B 31 FE1 SF4 B 73 1555 1555 2.12 LINK SG CYS B 34 FE2 SF4 B 73 1555 1555 2.28 LINK SG CYS B 48 FE3 SF4 B 73 1555 1555 2.11
SITE 1 AC1 5 CYS A 31 CYS A 34 PHE A 36 CYS A 48 SITE 2 AC1 5 CYS A 64 SITE 1 AC2 4 CYS B 31 CYS B 34 CYS B 48 CYS B 64
CRYST1 60.000 31.940 40.270 90.00 100.50 90.00 P 1 21 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 0.016667 0.000000 0.003089 0.00000
SCALE2 0.000000 0.031309 0.000000 0.00000
SCALE3 0.000000 0.000000 0.025255 0.00000